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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:ETLS20230067. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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2
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Chiwina K, Xiong H, Bhattarai G, Dickson RW, Phiri TM, Chen Y, Alatawi I, Dean D, Joshi NK, Chen Y, Riaz A, Gepts P, Brick M, Byrne PF, Schwartz H, Ogg JB, Otto K, Fall A, Gilbert J, Shi A. Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection. Int J Mol Sci 2023; 24:15300. [PMID: 37894980 PMCID: PMC10607830 DOI: 10.3390/ijms242015300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for Fop race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved Fop resistance.
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Affiliation(s)
- Kenani Chiwina
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Ryan William Dickson
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Theresa Makawa Phiri
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Ibtisam Alatawi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Derek Dean
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Neelendra K. Joshi
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Yuyan Chen
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Awais Riaz
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Paul Gepts
- Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA;
| | - Mark Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Patrick F. Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Howard Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; (H.S.); (K.O.)
| | - James B. Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Kristin Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; (H.S.); (K.O.)
| | - Amy Fall
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Jeremy Gilbert
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
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3
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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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Wong CYS, Jones T, McHugh DP, Gilbert ME, Gepts P, Palkovic A, Buckley TN, Magney TS. TSWIFT: Tower Spectrometer on Wheels for Investigating Frequent Timeseries for high-throughput phenotyping of vegetation physiology. Plant Methods 2023; 19:29. [PMID: 36978119 PMCID: PMC10044391 DOI: 10.1186/s13007-023-01001-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Remote sensing instruments enable high-throughput phenotyping of plant traits and stress resilience across scale. Spatial (handheld devices, towers, drones, airborne, and satellites) and temporal (continuous or intermittent) tradeoffs can enable or constrain plant science applications. Here, we describe the technical details of TSWIFT (Tower Spectrometer on Wheels for Investigating Frequent Timeseries), a mobile tower-based hyperspectral remote sensing system for continuous monitoring of spectral reflectance across visible-near infrared regions with the capacity to resolve solar-induced fluorescence (SIF). RESULTS We demonstrate potential applications for monitoring short-term (diurnal) and long-term (seasonal) variation of vegetation for high-throughput phenotyping applications. We deployed TSWIFT in a field experiment of 300 common bean genotypes in two treatments: control (irrigated) and drought (terminal drought). We evaluated the normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), and SIF, as well as the coefficient of variation (CV) across the visible-near infrared spectral range (400 to 900 nm). NDVI tracked structural variation early in the growing season, following initial plant growth and development. PRI and SIF were more dynamic, exhibiting variation diurnally and seasonally, enabling quantification of genotypic variation in physiological response to drought conditions. Beyond vegetation indices, CV of hyperspectral reflectance showed the most variability across genotypes, treatment, and time in the visible and red-edge spectral regions. CONCLUSIONS TSWIFT enables continuous and automated monitoring of hyperspectral reflectance for assessing variation in plant structure and function at high spatial and temporal resolutions for high-throughput phenotyping. Mobile, tower-based systems like this can provide short- and long-term datasets to assess genotypic and/or management responses to the environment, and ultimately enable the spectral prediction of resource-use efficiency, stress resilience, productivity and yield.
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Affiliation(s)
| | - Taylor Jones
- Department of Earth & Environment, Boston University, Boston, MA 02215 USA
| | - Devin P. McHugh
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Matthew E. Gilbert
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Antonia Palkovic
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Thomas N. Buckley
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Troy S. Magney
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
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5
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Wong CYS, Gilbert ME, Pierce MA, Parker TA, Palkovic A, Gepts P, Magney TS, Buckley TN. Hyperspectral Remote Sensing for Phenotyping the Physiological Drought Response of Common and Tepary Bean. Plant Phenomics 2023; 5:0021. [PMID: 37040284 PMCID: PMC10076057 DOI: 10.34133/plantphenomics.0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/12/2022] [Indexed: 06/19/2023]
Abstract
Proximal remote sensing offers a powerful tool for high-throughput phenotyping of plants for assessing stress response. Bean plants, an important legume for human consumption, are often grown in regions with limited rainfall and irrigation and are therefore bred to further enhance drought tolerance. We assessed physiological (stomatal conductance and predawn and midday leaf water potential) and ground- and tower-based hyperspectral remote sensing (400 to 2,400 nm and 400 to 900 nm, respectively) measurements to evaluate drought response in 12 common bean and 4 tepary bean genotypes across 3 field campaigns (1 predrought and 2 post-drought). Hyperspectral data in partial least squares regression models predicted these physiological traits (R 2 = 0.20 to 0.55; root mean square percent error 16% to 31%). Furthermore, ground-based partial least squares regression models successfully ranked genotypic drought responses similar to the physiologically based ranks. This study demonstrates applications of high-resolution hyperspectral remote sensing for predicting plant traits and phenotyping drought response across genotypes for vegetation monitoring and breeding population screening.
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Barrera S, Berny Mier y Teran JC, Lobaton JD, Escobar R, Gepts P, Beebe S, Urrea CA. Large genomic introgression blocks of Phaseolus parvifolius Freytag bean into the common bean enhance the crossability between tepary and common beans. Plant Direct 2022; 6:e470. [PMID: 36523608 PMCID: PMC9745863 DOI: 10.1002/pld3.470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 06/10/2023]
Abstract
The production of the common bean (Phaseolus vulgaris L.), one of the most important sources of protein and minerals and one of the most consumed grain legumes globally, is highly affected by heat and drought constraints. In contrast, the tepary bean (Phaseolus acutifolius A. Gray), a common bean-related species, is adapted to hot and dry climates. Hybridization to introduce complex traits from the tepary bean into the common bean has been challenging, as embryo rescue is required. In this study, we report three novel interspecific lines that were obtained by crossing lines from prior common bean × tepary bean hybridization with Phaseolus parvifolius Freytag in order to increase the male gametic diversity to facilitate interspecific crosses. These interspecific lines enhanced the crossability of the common bean and tepary bean species while avoiding the embryo rescue process. Crossing these three interspecific lines with tepary beans resulted in 12-fold more hybrid plants than crossing traditional common beans with tepary beans. Whole-genome sequencing analysis of these three interspecific lines shows large introgressions of genomic regions corresponding to P. parvifolius on chromosomes that presumably contribute to reproductive barriers between both species. The development of these lines opens up the possibility of increasing the introgression of desirable tepary bean traits into the common bean to address constraints driven by climate change.
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Affiliation(s)
- Santos Barrera
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNebraskaUSA
| | | | - Juan David Lobaton
- Department of Evolutionary BiologyNational Australian UniversityCanberraAustralia
| | | | - Paul Gepts
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Steve Beebe
- International Center for Tropical Agriculture (CIAT)PalmiraColombia
| | - Carlos A. Urrea
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNebraskaUSA
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Parker TA, Cetz J, de Sousa LL, Kuzay S, Lo S, Floriani TDO, Njau S, Arunga E, Duitama J, Jernstedt J, Myers JR, Llaca V, Herrera-Estrella A, Gepts P. Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion and overexpression of PvIND. New Phytol 2022; 235:2454-2465. [PMID: 35708662 DOI: 10.1111/nph.18319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris), the principal global grain legume staple, two main production categories are distinguished by fibre deposition in pods: dry beans, with fibrous, stringy pods; and stringless snap/green beans, with reduced fibre deposition, which frequently revert to the ancestral stringy state. Here, we identify genetic and developmental patterns associated with pod fibre deposition. Transcriptional, anatomical, epigenetic and genetic regulation of pod strings were explored through RNA-seq, RT-qPCR, fluorescence microscopy, bisulfite sequencing and whole-genome sequencing. Overexpression of the INDEHISCENT ('PvIND') orthologue was observed in stringless types compared with isogenic stringy lines, associated with overspecification of weak dehiscence-zone cells throughout the pod vascular sheath. No differences in DNA methylation were correlated with this phenotype. Nonstringy varieties showed a tandemly direct duplicated PvIND and a Ty1-copia retrotransposon inserted between the two repeats. These sequence features are lost during pod reversion and are predictive of pod phenotype in diverse materials, supporting their role in PvIND overexpression and reversible string phenotype. Our results give insight into reversible gain-of-function mutations and possible genetic solutions to the reversion problem, of considerable economic value for green bean production.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Jose Cetz
- National Laboratory of Genomics for Biodiversity, CINVESTAV, Irapuato, Guanajuato, C.P. 36821, Mexico
| | - Lorenna Lopes de Sousa
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Saarah Kuzay
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Sassoum Lo
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Talissa de Oliveira Floriani
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
- Department of Genetics, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Serah Njau
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
- Department of Water and Agricultural Resource Management, University of Embu, Embu, 60100, Kenya
| | - Esther Arunga
- Department of Water and Agricultural Resource Management, University of Embu, Embu, 60100, Kenya
| | - Jorge Duitama
- Department of Systems and Computing Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Judy Jernstedt
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - James R Myers
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Alfredo Herrera-Estrella
- National Laboratory of Genomics for Biodiversity, CINVESTAV, Irapuato, Guanajuato, C.P. 36821, Mexico
| | - Paul Gepts
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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9
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Nalupya Z, Hamabwe S, Mukuma C, Lungu D, Gepts P, Kamfwa K. Characterization of Colletotrichum lindemuthianum Races in Zambia and Evaluation of the CIAT Phaseolus Core Collection for Resistance to Anthracnose. Plant Dis 2021; 105:3939-3945. [PMID: 33988467 DOI: 10.1094/pdis-02-21-0363-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Colletotrichum lindemuthianum, the causal pathogen of common bean (Phaseolus vulgaris) anthracnose, is highly variable. Therefore, understanding its race structure and identification of new sources of resistance is necessary for the development of varieties with durable resistance. The objectives of this study were (i) to characterize isolates of C. lindemuthianum collected from three major bean-growing regions in Zambia and (ii) evaluate the International Center for Tropical Agriculture (CIAT) Phaseolus core collection for resistance to C. lindemuthianum races 37, 73, and 566 and a blend of 20 races. Isolates collected from three major bean-growing districts in Zambia, namely Mporokoso, Mpika, and Mbala, were characterized as races 37, 73, and 566, respectively. A subset of the CIAT core collection comprising 885 accessions of common bean, 13 accessions of scarlet runner bean (Phaseolus coccineus), and 11 accessions of year bean (Phaseolus dumosus) was evaluated for resistance to races 37, 73, and 566 and a blend of 20 races in a greenhouse at the University of Zambia, Lusaka, Zambia. Totals of 72, 66, 48, and 9% of P. vulgaris accessions evaluated were highly resistant to races 37, 73, and 566 and a blend of 20 races, respectively. Also, accessions of P. coccineus and P. dumosus highly resistant to races 37, 73, and 566 were identified. Only eight of the 331 P. vulgaris accessions were highly resistant to all three individual races (37, 73, and 566) and to a blend of 20 races. These eight accessions constitute a valuable breeding resource for developing varieties with durable resistance to C. lindemuthianum.
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Affiliation(s)
- Zombe Nalupya
- Department of Plant Sciences, University of Zambia, Lusaka, Zambia
| | - Swivia Hamabwe
- Department of Plant Sciences, University of Zambia, Lusaka, Zambia
| | | | - Davis Lungu
- Department of Plant Sciences, University of Zambia, Lusaka, Zambia
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Kelvin Kamfwa
- Department of Plant Sciences, University of Zambia, Lusaka, Zambia
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10
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Delfini J, Moda-Cirino V, dos Santos Neto J, Zeffa DM, Nogueira AF, Ribeiro LAB, Ruas PM, Gepts P, Gonçalves LSA. Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean. Front Plant Sci 2021; 12:748829. [PMID: 34691125 PMCID: PMC8528967 DOI: 10.3389/fpls.2021.748829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/15/2021] [Indexed: 05/25/2023]
Abstract
The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.
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Affiliation(s)
- Jessica Delfini
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Vânia Moda-Cirino
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
| | - José dos Santos Neto
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Douglas Mariani Zeffa
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Alison Fernando Nogueira
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Luriam Aparecida Brandão Ribeiro
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Paulo Maurício Ruas
- Departamento de Biologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Leandro Simões Azeredo Gonçalves
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
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11
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Lo S, Parker T, Muñoz-Amatriaín M, Berny-Mier Y Teran JC, Jernstedt J, Close TJ, Gepts P. Genetic, anatomical, and environmental patterns related to pod shattering resistance in domesticated cowpea [Vigna unguiculata (L.) Walp]. J Exp Bot 2021; 72:6219-6229. [PMID: 34106233 DOI: 10.1093/jxb/erab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/06/2021] [Indexed: 05/27/2023]
Abstract
Pod shattering, which causes the explosive release of seeds from the pod, is one of the main sources of yield losses in cowpea in arid and semi-arid areas. Reduction of shattering has therefore been a primary target for selection during domestication and improvement of cowpea, among other species. Using a mini-core diversity panel of 368 cowpea accessions, four regions with a statistically significant association with pod shattering were identified. Two genes (Vigun03g321100 and Vigun11g100600), involved in cell wall biosynthesis, were identified as strong candidates for pod shattering. Microscopic analysis was conducted on a subset of accessions representing the full spectrum of shattering phenotypes. This analysis indicated that the extent of wall fiber deposition was highly correlated with shattering. The results from this study also demonstrate that pod shattering in cowpea is exacerbated by arid environmental conditions. Finally, using a subset of West African landraces, patterns of historical selection for shattering resistance related to precipitation in the environment of origin were identified. Together, these results shed light on sources of resistance to pod shattering, which will, in turn, improve climate resilience of a major global nutritional staple.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - Travis Parker
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523,USA
| | | | - Judy Jernstedt
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
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12
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Delfini J, Moda-Cirino V, Dos Santos Neto J, Zeffa DM, Nogueira AF, Ribeiro LAB, Ruas PM, Gepts P, Gonçalves LSA. Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel. Theor Appl Genet 2021; 134:2795-2811. [PMID: 34027567 DOI: 10.1007/s00122-021-03859-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
QTNs significantly associated to nine mineral content in grains of common bean were identified. The accumulation of favorable alleles was associated with a gradually increasing nutrient content in the grain. Biofortification is one of the strategies developed to address malnutrition in developing countries, the aim of which is to improve the nutritional content of crops. The common bean (Phaseolus vulgaris L.), a staple food in several African and Latin American countries, has excellent nutritional attributes and is considered a strong candidate for biofortification. The objective of this study was to identify genomic regions associated with nutritional content in common bean grains using 178 Mesoamerican accessions belonging to a Brazilian Diversity Panel (BDP) and 25,011 good-quality single nucleotide polymorphisms. The BDP was phenotyped in three environments for nine nutrients (phosphorus, potassium, calcium, magnesium, copper, manganese, sulfur, zinc, and iron) using four genome-wide association multi-locus methods. To obtain more accurate results, only quantitative trait nucleotides (QTNs) that showed repeatability (i.e., those detected at least twice using different methods or environments) were considered. Forty-eight QTNs detected for the nine minerals showed repeatability and were considered reliable. Pleiotropic QTNs and overlapping genomic regions surrounding the QTNs were identified, demonstrating the possible association between the deposition mechanisms of different nutrients in grains. The accumulation of favorable alleles in the same accession was associated with a gradually increasing nutrient content in the grain. The BDP proved to be a valuable source for association studies. The investigation of different methods and environments showed the reliability of markers associated with minerals. The loci identified in this study will potentially contribute to the improvement of Mesoamerican common beans, particularly carioca and black beans, the main groups consumed in Brazil.
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Affiliation(s)
- Jessica Delfini
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Vânia Moda-Cirino
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
| | - José Dos Santos Neto
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Douglas Mariani Zeffa
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Alison Fernando Nogueira
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Luriam Aparecida Brandão Ribeiro
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Paulo Maurício Ruas
- Biology Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Leandro Simões Azeredo Gonçalves
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil.
- Agronomy Department, Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
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13
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Elias JCF, Gonçalves-Vidigal MC, Ariani A, Valentini G, Martiniano-Souza MDC, Vaz Bisneta M, Gepts P. Genome-Environment Association Analysis for Bio-Climatic Variables in Common Bean ( Phaseolus vulgaris L.) from Brazil. Plants (Basel) 2021; 10:plants10081572. [PMID: 34451617 PMCID: PMC8399474 DOI: 10.3390/plants10081572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 05/08/2023]
Abstract
Abiotic stress is a limiting factor for common bean (Phaseolus vulgaris L.) production globally. The study of the genotypic, phenotypic, and bio-climatic variables in a broad set of accessions may assist the identification of genomic regions involved in the climatic adaptation of the common bean. We conducted a genotyping-by-sequencing analysis using 28,823 SNPs on 110 georeferenced common bean accessions from Brazil to discover associations between SNPs and bio-climatic indexes. The population structure analysis clustered the accessions into two groups corresponding to the Andean and Mesoamerican gene pools. Of the 19 bioclimatic variables, 17 exhibited a significant association with SNPs on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, Pv09, Pv10, and Pv11 of common bean. Ten candidate genes were associated with specific bio-climatic variables related to temperature and precipitation. The candidate genes associated with this significant Pv09 region encode a Platz transcription factor family protein previously reported to be an essential regulator of drought stress. The SNP markers and candidate genes associated with the bio-climatic variables should be validated in segregating populations for water stress, which could further be used for marker-assisted selection. As a result, bean breeding programs may be able to provide advances in obtaining drought-tolerant cultivars.
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Affiliation(s)
- Júlio Cesar F. Elias
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Maria Celeste Gonçalves-Vidigal
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
- Correspondence: ; Tel.:+55-449-9908-8186
| | | | - Giseli Valentini
- Soybean Genomics and Improvement Laboratory USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA;
| | - Maria da Conceição Martiniano-Souza
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95161-8780, USA;
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Parker TA, Lo S, Gepts P. Pod shattering in grain legumes: emerging genetic and environment-related patterns. 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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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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. Plant J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Garcia T, Duitama J, Zullo SS, Gil J, Ariani A, Dohle S, Palkovic A, Skeen P, Bermudez-Santana CI, Debouck DG, Martínez-Castillo J, Gepts P, Chacón-Sánchez MI. Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 2021; 12:702. [PMID: 33514713 PMCID: PMC7846787 DOI: 10.1038/s41467-021-20921-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
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Affiliation(s)
- Tatiana Garcia
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,grid.17088.360000 0001 2150 1785Present Address: Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI USA
| | - Jorge Duitama
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Stephanie Smolenski Zullo
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Juanita Gil
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia ,grid.411017.20000 0001 2151 0999Present Address: Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR USA
| | - Andrea Ariani
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA ,Present Address: BASF BBCC - Innovation Center, Gent, Belgium
| | - Sarah Dohle
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Antonia Palkovic
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Paola Skeen
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,Present Address: Nunhems USA, Vegetable Seeds BASF, Acampo, CA USA
| | - Clara Isabel Bermudez-Santana
- grid.10689.360000 0001 0286 3748Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel G. Debouck
- grid.418348.20000 0001 0943 556XCentro Internacional de Agricultura Tropical, Cali, Colombia
| | - Jaime Martínez-Castillo
- grid.418270.80000 0004 0428 7635Centro de Investigación Científica de Yucatán, Yucatán, Mexico
| | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Maria Isabel Chacón-Sánchez
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
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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. Theor Appl Genet 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lo S, Fatokun C, Boukar O, Gepts P, Close TJ, Muñoz-Amatriaín M. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). PLoS One 2020; 15:e0229167. [PMID: 32343700 PMCID: PMC7188242 DOI: 10.1371/journal.pone.0229167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Perennial habit and floral scent are major traits that distinguish domesticated cowpeas from their wild relatives. However, the genetic basis of these two important traits remains largely unknown in cowpea. Plant longevity, a perenniality-related trait, and floral scent, an outcrossing trait, were investigated using a RIL population derived from a cross between a domesticated and a wild cowpea. QTL analysis revealed three significant loci, one on chromosome 8 associated with plant longevity and two, on chromosomes 1 and 11, for floral scent. Genes within the QTL regions were identified. Genes encoding an F-box protein (Vigun08g215300) and two kinases (Vigun08g217000, Vigun08g217800), and involved in physiological processes including regulation of flowering time and plant longevity, were identified within the perenniality QTL region. A cluster of O-methyltransferase genes (Vigun11g096800, Vigun11g096900, Vigun11g097000, Vigun11g097600, and Vigun11g097800) was identified within the floral scent QTL region. These O-methyltransferase cowpea genes are orthologs of the Arabidopsis N-acetylserotonin O-methyltransferase (ASMT) gene, which is involved in the biosynthesis of melatonin. Melatonin is an indole derivative, which is an essential molecule for plant interactions with pollinators. These findings lay the foundation for further exploration of the genetic mechanisms of perenniality and floral scent in cowpea. Knowledge from this study can help in the development of new extended-growth cycle lines with increased yield or lines with increased outcrossing for population breeding.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States of America
- * E-mail: (MMA); (SL)
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Paul Gepts
- Department of Plant Sciences, University of California Davis, Davis, CA, United States of America
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States of America
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
- * E-mail: (MMA); (SL)
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Berny Mier y Teran JC, Konzen ER, Palkovic A, Tsai SM, Gepts P. Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations. Front Plant Sci 2020; 11:346. [PMID: 32308660 PMCID: PMC7145959 DOI: 10.3389/fpls.2020.00346] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/29/2023]
Abstract
Genetic analyses and utilization of wild genetic variation for crop improvement in common bean (Phaseolus vulgaris L.) have been hampered by yield evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to cultivation conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild variation within a more adapted background. Three domesticated by wild backcrossed-inbred-line populations (BC1S4) were developed using three wild accessions representing the full range of rainfall of the Mesoamerican wild bean distribution crossed to the elite drought tolerant domesticated parent SEA 5. These populations were evaluated under field conditions in three environments, two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The goal was to test if these populations responded differently to drought stress and contained progenies with higher yield than SEA 5, not only under drought but also under water-watered conditions. Results revealed that the two populations derived from wild parents of the lower rainfall regions produced lines with higher yield compared to the domesticated parent in the three environments, i.e., both in the drought-stressed environment and in the well-watered treatments. Several progeny lines produced yields, which on average over the three environments were 20% higher than the SEA 5 yield. Twenty QTLs for yield were identified in 13 unique regions on eight of the 11 chromosomes of common bean. Five of these regions showed at least one wild allele that increased yield over the domesticated parent. The variation explained by these QTLs ranged from 0.6 to 5.4% of the total variation and the additive effects ranged from -164 to 277 kg ha-1, with evidence suggesting allelic series for some QTLs. Our results underscore the potential of wild variation, especially from drought-stressed regions, for bean crop improvement as well the identification of regions for efficient marker-assisted introgression.
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Affiliation(s)
| | - Enéas R. Konzen
- Cell and Molecular Biology Laboratory, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Antonia Palkovic
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Siu M. Tsai
- Cell and Molecular Biology Laboratory, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Parker TA, Berny Mier Y Teran JC, Palkovic A, Jernstedt J, Gepts P. Pod indehiscence is a domestication and aridity resilience trait in common bean. New Phytol 2020; 225:558-570. [PMID: 31486530 DOI: 10.1111/nph.16164] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/14/2019] [Indexed: 05/05/2023]
Abstract
Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display atavistic characteristics that were advantageous to their wild ancestors but are deleterious under cultivation, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in the common bean (Phaseolus vulgaris), a major domesticated grain legume. Using three methods to evaluate the PD phenotype, we identified multiple, unlinked genetic regions controlling PD in a biparental population and two diversity panels. Subsequently, we assessed patterns of orthology among these loci and those controlling the trait in other species. Our results show that different genes were selected in each domestication and ecogeographic race. A chromosome Pv03 dirigent-like gene, involved in lignin biosynthesis, showed a base-pair substitution that is associated with decreased PD. This haplotype may underlie the expansion of Mesoamerican domesticates into northern Mexico, where arid conditions promote PD. The rise in frequency of the decreased-PD haplotype may be a consequence of the markedly different fitness landscape imposed by domestication. Environmental dependency and genetic redundancy can explain the maintenance of atavistic traits under domestication.
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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, USA
| | - Jorge C Berny Mier Y Teran
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Antonia Palkovic
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Judy Jernstedt
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Paul Gepts
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
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23
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Berny Mier y Teran JC, Konzen ER, Medina V, Palkovic A, Ariani A, Tsai SM, Gilbert ME, Gepts P. Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.). Ann Bot 2019; 124:917-932. [PMID: 30596881 PMCID: PMC6881220 DOI: 10.1093/aob/mcy221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/14/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. METHODS An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. RESULTS Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. CONCLUSIONS The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.
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Affiliation(s)
- Jorge C Berny Mier y Teran
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Enéas R Konzen
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brasil
| | - Viviana Medina
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Antonia Palkovic
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Andrea Ariani
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brasil
| | - Matthew E Gilbert
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - P Gepts
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
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Berny Mier Y Teran JC, Konzen ER, Palkovic A, Tsai SM, Rao IM, Beebe S, Gepts P. Effect of drought stress on the genetic architecture of photosynthate allocation and remobilization in pods of common bean (Phaseolus vulgaris L.), a key species for food security. BMC Plant Biol 2019; 19:171. [PMID: 31039735 PMCID: PMC6492436 DOI: 10.1186/s12870-019-1774-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/11/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed quality. Previous studies have shown that photosynthate remobilization and partitioning is one of the main mechanisms of drought tolerance and overall productivity in common bean. RESULTS In this study, we sought to determine the inheritance of pod harvest index (PHI), a measure of the partitioning of pod biomass to seed biomass, relative to that of grain yield. We evaluated a recombinant inbred population of the cross of ICA Bunsi and SXB405, both from the Mesoamerican gene pool, to determine the effects of intermittent and terminal drought stresses on the genetic architecture of photosynthate allocation and remobilization in pods of common bean. The population was grown for two seasons, under well-watered conditions and terminal and intermittent drought stress in one year, and well-watered conditions and terminal drought stress in the second year. There was a significant effect of the water regime and year on all the traits, at both the phenotypic and QTL levels. We found nine QTLs for pod harvest index, including a major (17% of variation explained), stable QTL on linkage group Pv07. We also found eight QTLs for yield, three of which clustered with PHI QTLs, underscoring the importance of photosynthate remobilization in productivity. We also found evidence for substantial epistasis, explaining a considerable part of the variation for yield and PHI. CONCLUSION Our results highlight the genetic relationship between PHI and yield and confirm the role of PHI in selection of both additive and epistatic effects controlling drought tolerance. These results are a key component to strengthen the robustness of common bean against drought stresses.
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Affiliation(s)
| | - Enéas R Konzen
- Department of Plant Sciences, University of California, Davis, CA, USA
- Cell and Molecular Biology Laboratory, Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brazil
- Present Address: Universidade Federal do Rio Grande do Sul, Campus Litoral Norte, Imbé, RS, Brazil
| | - Antonia Palkovic
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Idupulapati M Rao
- Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
- United States Department of Agriculture, Plant Polymer Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, Il, USA
| | - Stephen Beebe
- Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, USA.
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Abstract
Crop biodiversity is one of the major inventions of humanity through the process of domestication. It is also an essential resource for crop improvement to adapt agriculture to ever-changing conditions like global climate change and consumer preferences. Domestication and the subsequent evolution under cultivation have profoundly shaped the genetic architecture of this biodiversity. In this review, we highlight recent advances in our understanding of crop biodiversity. Topics include the reduction of genetic diversity during domestication and counteracting factors, a discussion of the relationship between parallel phenotypic and genotypic evolution, the role of plasticity in genotype × environment interactions, and the important role subsistence farmers play in actively maintaining crop biodiversity and in participatory breeding. Linking genotype and phenotype remains the holy grail of crop biodiversity studies.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020, USA;
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California 95616-8780, USA; ,
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26
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Abstract
The wild progenitor of common-bean has an exceptionally large distribution from northern Mexico to northwestern Argentina, unusual among crop wild progenitors. This research sought to document major events of range expansion that led to this distribution and associated environmental changes. Through the use of genotyping-by-sequencing (∼20,000 SNPs) and geographic information systems applied to a sample of 246 accessions of wild Phaseolus vulgaris, including 157 genotypes of the Mesoamerican, 77 of the southern Andean, and 12 of the Northern Peru–Ecuador gene pools, we identified five geographically distinct subpopulations. Three of these subpopulations belong to the Mesoamerican gene pool (Northern and Central Mexico, Oaxaca, and Southern Mexico, Central America and northern South America) and one each to the Northern Peru–Ecuador (PhI) and the southern Andean gene pools. The five subpopulations were distributed in different floristic provinces of the Neotropical seasonally dry forest and showed distinct distributions for temperature and rainfall resulting in decreased local potential evapotranspiration (PhI and southern Andes groups) compared with the two Mexican groups. Three of these subpopulations represent long-distance dispersal events from Mesoamerica into Northern Peru–Ecuador, southern Andes, and Central America and Colombia, in chronological order. Of particular note is that the dispersal to Northern Peru–Ecuador markedly predates the dispersal to the southern Andes (∼400 vs. ∼100 ky), consistent with the ancestral nature of the phaseolin seed protein and chloroplast sequences observed in the PhI group. Seed dispersal in common bean can be, therefore, described at different spatial and temporal scales, from localized, annual seed shattering to long‐distance, evolutionarily rare migration.
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Affiliation(s)
- Andrea Ariani
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA
| | | | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA
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Gioia T, Logozzo G, Marzario S, Spagnoletti Zeuli P, Gepts P. Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris). PLoS One 2019; 14:e0211342. [PMID: 30703134 PMCID: PMC6354994 DOI: 10.1371/journal.pone.0211342] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/13/2019] [Indexed: 01/31/2023] Open
Abstract
Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups-black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.
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Affiliation(s)
- Tania Gioia
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, Davis, CA, United States of America
| | - Giuseppina Logozzo
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Stefania Marzario
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Pierluigi Spagnoletti Zeuli
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Paul Gepts
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, Davis, CA, United States of America
- * E-mail:
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Okii D, Badji A, Odong T, Talwana H, Tukamuhabwa P, Male A, Mukankusi C, Gepts P. Recombination fraction and genetic linkage among key disease resistance genes ( Co-42 / Phg-2 and Co-5/"P.ult") in common bean. ACTA ACUST UNITED AC 2019; 18:AJB-18-29-819. [PMID: 33281892 PMCID: PMC7672375 DOI: 10.5897/ajb2019.16776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/26/2019] [Indexed: 10/31/2022]
Abstract
Anthracnose (Colletotrichum lindemuthianum), Angular leaf spot (Pseudocercospora griseola) and Pythium root rot are important pathogens affecting common bean production in the tropics. A promising strategy to manage these diseases consists of combining several resistance (R) genes into one cultivar. The aim of the study was to determine genetic linkage between gene pairs, Co-42 /Phg-2, on bean-chromosome Pv08 and Co-5/"P.ult" on-chromosome Pv07, to increase the efficiency of dual selection of resistance genes for major bean diseases, with molecular markers. The level of recombination was determined by tracking molecular markers for both BC3F6 and F2 generations. Recombination fraction r, among gene pairs, the likelihood of linkage, L(r), and logarithm of odds (LOD) scores were computed using the statistical relationship of likelihood which assumes a binomial distribution. The SCAR marker pair SAB3/PYAA19 for the gene pair Co-5/"P.ult" exhibited moderate linkage (r = 32 cM with a high LOD score of 9.2) for BC3F6 population, but relatively stronger linkage for the F2 population (r = 21 cM with a high LOD score of 18.7). However, the linkage among SCAR marker pair SH18/SN02, for the gene pair Co-42 /Phg-2 was incomplete for BC3F6 population (r = 47 cM with a low LOD score of 0.16) as well as F2 population (r = 44 cM with a low LOD score of 0.7). Generally, the weak or incomplete genetic linkage between marker pairs studied showed that all the four genes mentioned earlier have to be tagged with a corresponding linked marker during selection. The approaches used in this study will contribute to two loci linkage mapping techniques in segregating plant populations.
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Affiliation(s)
- Dennis Okii
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Arfang Badji
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Thomas Odong
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Herbert Talwana
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Phinehas Tukamuhabwa
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Allan Male
- International Centre for Tropical Agriculture (CIAT)/Pan African Bean Research Alliance (PABRA), P. O. Box 6247, Kampala, Uganda
| | - Clare Mukankusi
- International Centre for Tropical Agriculture (CIAT)/Pan African Bean Research Alliance (PABRA), P. O. Box 6247, Kampala, Uganda
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA 95616-8780, USA
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Lobaton JD, Miller T, Gil J, Ariza D, de la Hoz JF, Soler A, Beebe S, Duitama J, Gepts P, Raatz B. Resequencing of Common Bean Identifies Regions of Inter-Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding. Plant Genome 2018; 11. [PMID: 30025029 DOI: 10.3835/plantgenome2017.08.0068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A. Gray), and L. were sequenced by whole-genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between and the two other domesticated species, but also within , affecting hundreds of protein-coding genomic regions. A large number of inter-gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
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Dequigiovanni G, Ramos SLF, Alves-Pereira A, Fabri EG, Picanço-Rodrigues D, Clement CR, Gepts P, Veasey EA. Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia. PLoS One 2018; 13:e0198593. [PMID: 29874280 PMCID: PMC5991381 DOI: 10.1371/journal.pone.0198593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/22/2018] [Indexed: 01/19/2023] Open
Abstract
Annatto (Bixa orellana L.) is a tropical American crop, commercially valuable due to its application in the food and cosmetics industries as a natural dye. The wild ancestor of cultivated annatto is B. orellana var. urucurana. Although never cultivated, this variety occurs in open forests and anthropogenic landscapes, and is always associated with riparian environments. In this study, we evaluated the genetic diversity and structure of B. orellana var. urucurana populations in Brazilian Amazonia using 16 microsatellite loci. We used Ecological Niche Modeling (ENM) to characterize the potential geographical range of this variety in northern South America. We analyzed 170 samples from 10 municipalities in the states of Rondônia, Pará and Roraima. A total of 194 alleles was observed, with an average of 12.1 alleles per locus. Higher levels of expected (HE) than observed (HO) heterozygosities were found for all populations. Bayesian analysis, Neighbor-Joining dendrograms and PCAs suggest the existence of three strongly structured groups of populations. A strong and positive correlation between genetic and geographic distances was found, suggesting that genetic differentiation might be caused by geographic isolation. From species distribution modelling, we detected that South Rondônia, Madre di Dios River basin, Llanos de Mojos, Llanos de Orinoco and eastern Ecuador are highly suitable areas for wild annatto to occur, providing additional targets for future exploration and conservation. Climatic adaptation analyses revealed strong differentiation among populations, suggesting that precipitation plays a key role in wild annatto’s current and potential distribution patterns.
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Affiliation(s)
- Gabriel Dequigiovanni
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
| | | | - Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
| | - Eliane Gomes Fabri
- Centro de Horticultura, Instituto Agronômico de Campinas, Campinas, São Paulo, Brasil
| | - Doriane Picanço-Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (ICB-UFAM), Manaus, Amazonas, Brasil
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
- * E-mail:
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Wilkus EL, Berny Mier y Teran JC, Mukankusi CM, Gepts P. Genetic Patterns of Common-Bean Seed Acquisition and Early-Stage Adoption Among Farmer Groups in Western Uganda. Front Plant Sci 2018; 9:586. [PMID: 29868053 PMCID: PMC5958309 DOI: 10.3389/fpls.2018.00586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Widespread adoption of new varieties can be valuable, especially where improved agricultural production technologies are hard to access. However, as farmers adopt new varieties, in situ population structure and genetic diversity of their seed holdings can change drastically. Consequences of adoption are still poorly understood due to a lack of crop genetic diversity assessments and detailed surveys of farmers' seed management practices. Common bean (Phaseolus vulgaris) is an excellent model for these types of studies, as it has a long history of cultivation among smallholder farmers, exhibits eco-geographic patterns of diversity (e.g., Andean vs. Mesoamerican gene-pools), and has been subjected to post-Columbian dispersal and recent introduction of improved cultivars. The Hoima district of western Uganda additionally provides an excellent social setting for evaluating consequences of adoption because access to improved varieties has varied across farmer groups in this production region. This study establishes a baseline understanding of the common bean diversity found among household producers in Uganda and compares the crop population structure, diversity and consequences of adoption of household producers with different adoption practices. Molecular diversity analysis, based on 4,955 single nucleotide polymorphism (SNP) markers, evaluated a total of 1,156 seed samples that included 196 household samples collected from household producers in the Hoima district, 19 breeder-selected varieties used in participatory breeding activities that had taken place prior to the study in the region, and a global bean germplasm collection. Households that had participated in regional participatory breeding efforts were more likely to adopt new varieties and, consequently, diversify their seed stocks than those that had not participated. Of the three farmer groups that participated in breeding efforts, households from the farmer group with the longest history of bean production were more likely to conserve "Seed Engufu", a local "Calima"-type variety of the Andean bean gene pool, and, at the same time, introduce rare Mesoamerican gene pool varieties into household seed stocks.
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Affiliation(s)
- Erin L. Wilkus
- Department of Plant Sciences, Section of Crop & Ecosystem Sciences, University of California, Davis, Davis, CA, United States
| | - Jorge C. Berny Mier y Teran
- Department of Plant Sciences, Section of Crop & Ecosystem Sciences, University of California, Davis, Davis, CA, United States
| | | | - Paul Gepts
- Department of Plant Sciences, Section of Crop & Ecosystem Sciences, University of California, Davis, Davis, CA, United States
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Rezene Y, Tesfaye K, Clare M, Male A, Gepts P. Rep-PCR Genomic Fingerprinting Revealed Genetic Diversity and Population Structure among Ethiopian Isolates of Pseudocercospora griseola Pathogen of the Common Bean (Phaseolus vulgaris L.). ACTA ACUST UNITED AC 2018. [DOI: 10.4172/2157-7471.1000463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biol 2017; 18:60. [PMID: 28356141 PMCID: PMC5370463 DOI: 10.1186/s13059-017-1190-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022] Open
Abstract
Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1190-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Josaphat M Montero-Vargas
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Soledad Saburido-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Anna Vlasova
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutierrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José Juan Ordaz-Ortiz
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | | | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, 95616-8780, USA
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
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de Araujo ASF, de Almeida Lopes AC, Teran JCBMY, Palkovic A, Gepts P. Nodulation ability in different genotypes of Phaseolus lunatus by rhizobia from California agricultural soils. Symbiosis 2016. [DOI: 10.1007/s13199-016-0465-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Espeland EK, Emery NC, Mercer KL, Woolbright SA, Kettenring KM, Gepts P, Etterson JR. Evolution of plant materials for ecological restoration: insights from the applied and basic literature. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12739] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Erin K. Espeland
- USDA-ARS Pest Management Research Unit; 1500 N. Central Avenue Sidney MT 59270 USA
| | - Nancy C. Emery
- Department of Ecology and Evolutionary Biology; RAMY 0334, University of Colorado; Boulder CO 80309 USA
| | - Kristin L. Mercer
- Department of Horticulture and Crop Science; 2021 Coffey Road, Ohio State University; Columbus OH 43210 USA
| | - Scott A. Woolbright
- Department of Biological Sciences; University of Arkansas at Little Rock 2801 S. University Avenue; Little Rock AR 72204 USA
| | - Karin M. Kettenring
- Ecology Center and Department of Watershed Sciences; 5210 Old Main Hill, Utah State University; Logan UT 84322 USA
| | - Paul Gepts
- Department of Plant Sciences/MS1; University of California; 1 Shields Avenue, Davis CA 95616 USA
| | - Julie R. Etterson
- Department of Biology; University of Minnesota Duluth; 1049 University Drive Duluth MN 55812 USA
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Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, de Oliveira AC, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Tuberosa R, Valliyodan B, Varshney RK, Yano M. Global agricultural intensification during climate change: a role for genomics. Plant Biotechnol J 2016; 14:1095-8. [PMID: 26360509 PMCID: PMC5049667 DOI: 10.1111/pbi.12467] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/23/2015] [Accepted: 08/06/2015] [Indexed: 05/03/2023]
Abstract
Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.
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Affiliation(s)
- Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jacqueline Batley
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia
| | | | - John Bryant
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed Association, Nasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | | | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agriculture, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Leland J Cseke
- Department of Biological Sciences Huntsville, The University of Alabama in Huntsville, Huntsville, AL, USA
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - David Edwards
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | | | - Robert Henry
- The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, Australia
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Glenn Thomas Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | | | - Mike Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - David Lightfoot
- College of Agricultural Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the Future, Kuala Lumpur, Malaysia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | - Rajeev K Varshney
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Centre of Excellence in Genomics, International Crops Research Institute for the Semi- Arid Tropics (ICRISAT), Hyderabad, India
| | - Masahiro Yano
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Japan
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Rodriguez M, Rau D, Bitocchi E, Bellucci E, Biagetti E, Carboni A, Gepts P, Nanni L, Papa R, Attene G. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris. New Phytol 2016; 209:1781-94. [PMID: 26526745 DOI: 10.1111/nph.13713] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/06/2015] [Indexed: 05/19/2023]
Abstract
Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.
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Affiliation(s)
- Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040, Alghero, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Eleonora Biagetti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Carboni
- Centro di Ricerca per le Colture Industriali (CRA-CIN), Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via di Corticella, 133, 40128, Bologna, Italy
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040, Alghero, Italy
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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Ariani A, Gepts P. Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.). Mol Genet Genomics 2015; 290:1771-85. [PMID: 25846963 DOI: 10.1007/s00438-015-1038-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/28/2015] [Indexed: 11/26/2022]
Abstract
Plant aquaporins are a large and diverse family of water channel proteins that are essential for several physiological processes in living organisms. Numerous studies have linked plant aquaporins with a plethora of processes, such as nutrient acquisition, CO2 transport, plant growth and development, and response to abiotic stresses. However, little is known about this protein family in common bean. Here, we present a genome-wide identification of the aquaporin gene family in common bean (Phaseolus vulgaris L.), a legume crop essential for human nutrition. We identified 41 full-length coding aquaporin sequences in the common bean genome, divided by phylogenetic analysis into five sub-families (PIPs, TIPs, NIPs, SIPs and XIPs). Residues determining substrate specificity of aquaporins (i.e., NPA motifs and ar/R selectivity filter) seem conserved between common bean and other plant species, allowing inference of substrate specificity for these proteins. Thanks to the availability of RNA-sequencing datasets, expression levels in different organs and in leaves of wild and domesticated bean accessions were evaluated. Three aquaporins (PvTIP1;1, PvPIP2;4 and PvPIP1;2) have the overall highest mean expressions, with PvTIP1;1 having the highest expression among all aquaporins. We performed an EST database mining to identify drought-responsive aquaporins in common bean. This analysis showed a significant increase in expression for PvTIP1;1 in drought stress conditions compared to well-watered environments. The pivotal role suggested for PvTIP1;1 in regulating water homeostasis and drought stress response in the common bean should be verified by further field experimentation under drought stress.
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Affiliation(s)
- Andrea Ariani
- Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA.
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
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Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 2014; 46:707-13. [PMID: 24908249 PMCID: PMC7048698 DOI: 10.1038/ng.3008] [Citation(s) in RCA: 690] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/15/2014] [Indexed: 01/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
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Affiliation(s)
- Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - G Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Steven B Cannon
- US Department of Agriculture–Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Qijian Song
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | | | - Valerie Geffroy
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
- Institut National de la Recherche Agronomique (INRA), Université Paris–Sud, Unité Mixte de Recherche de Génétique Végétale, Gif-sur-Yvette, France
| | - Samira Mafi Moghaddam
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Matthew Blair
- Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee USA
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Mansi Chovatia
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, California USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Michael Gonzales
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - David L Hyten
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Gaofeng Jia
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - James D Kelly
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan USA
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Manon M S Richard
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Phillip N Miklas
- US Department of Agriculture–Agricultural Research Service, Vegetable and Forage Crop Research Unit, Prosser, Washington USA
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Josiane Rodrigues
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Vincent Thareau
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Carlos A Urrea
- Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Ming Zhang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Rod A Wing
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Perry B Cregan
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Daniel S Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
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Gepts P. The contribution of genetic and genomic approaches to plant domestication studies. Curr Opin Plant Biol 2014; 18:51-9. [PMID: 24631844 DOI: 10.1016/j.pbi.2014.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/04/2014] [Accepted: 02/09/2014] [Indexed: 05/25/2023]
Abstract
The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.
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Affiliation(s)
- Paul Gepts
- University of California, Department of Plant Sciences/MS 1, Section of Crop and Ecosystem Sciences, 1 Shields Avenue, Davis, CA 95616, United States of America.
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Gonçalves-Vidigal MC, Cruz AS, Lacanallo GF, Vidigal Filho PS, Sousa LL, Pacheco CMNA, McClean P, Gepts P, Pastor-Corrales MA. Co-segregation analysis and mapping of the anthracnose Co-10 and angular leaf spot Phg-ON disease-resistance genes in the common bean cultivar Ouro Negro. Theor Appl Genet 2013; 126:2245-55. [PMID: 23760652 DOI: 10.1007/s00122-013-2131-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 05/21/2013] [Indexed: 05/03/2023]
Abstract
Anthracnose (ANT) and angular leaf spot (ALS) are devastating diseases of common bean (Phaseolus vulgaris L.). Ouro Negro is a highly productive common bean cultivar, which contains the Co-10 and Phg-ON genes for resistance to ANT and ALS, respectively. In this study, we performed a genetic co-segregation analysis of resistance to ANT and ALS using an F2 population from the Rudá × Ouro Negro cross and the F2:3 families from the AND 277 × Ouro Negro cross. Ouro Negro is resistant to races 7 and 73 of the ANT and race 63-39 of the ALS pathogens. Conversely, cultivars AND 277 and Rudá are susceptible to races 7 and 73 of ANT, respectively. Both cultivars are susceptible to race 63-39 of ALS. Co-segregation analysis revealed that Co-10 and Phg-ON were inherited together, conferring resistance to races 7 and 73 of ANT and race 63-39 of ALS. The Co-10 and Phg-ON genes were co-segregated and were tightly linked at a distance of 0.0 cM on chromosome Pv04. The molecular marker g2303 was linked to Co-10 and Phg-ON at a distance of 0.0 cM. Because of their physical linkage in a cis configuration, the Co-10 and Phg-ON resistance alleles are inherited together and can be monitored with great efficiency using g2303. The close linkage between the Co-10 and Phg-ON genes and prior evidence are consistent with the existence of a resistance gene cluster at one end of chromosome Pv04, which also contains the Co-3 locus and ANT resistance quantitative trait loci. These results will be very useful for breeding programs aimed at developing bean cultivars with ANT and ALS resistance using marker-assisted selection.
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Affiliation(s)
- M C Gonçalves-Vidigal
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, Brazil
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McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D. Agriculture: Feeding the future. Nature 2013; 499:23-4. [PMID: 23823779 DOI: 10.1038/499023a] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gioia T, Logozzo G, Kami J, Spagnoletti Zeuli P, Gepts P. Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common Bean. ACTA ACUST UNITED AC 2012; 104:273-86. [PMID: 23235700 DOI: 10.1093/jhered/ess102] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Reduction in pod shattering represents a key component of the domestication syndrome in common bean (Phaseolus vulgaris) and makes this domesticate dependent upon the farmer for seed dispersal. Attempts to elucidate the genetic control of this process have led to the identification of a major gene (St) linked to the presence/absence of pod suture fibers affecting pod shattering. Although St has been placed on the common bean genetic map, the sequence and the specific functions of this gene remain unknown. The purpose of this study was to identify a candidate gene for St. In Arabidopsis thaliana, INDEHISCENT gene (IND) is the primary factory required for silique shattering. A sequence homologous to IND was successfully amplified in P. vulgaris and placed on the common bean map using two recombinant inbred populations (BAT93 × Jalo EEP558; Midas × G12873). Although PvIND maps near the St locus, the lack of complete cosegregation between PvIND and St and the lack of polymorphisms at the PvIND locus correlated with the dehiscent/indehiscent phenotype suggests that PvIND may not be directly involved in pod shattering and may not be the gene underlying the St locus. However, PvIND may be closely linked to an as yet unidentified regulatory element at the St locus. Alternatively, a more precise phenotyping method taking into account quantitative trait variation needs to be developed to more accurately map the St locus.
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Affiliation(s)
- Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
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Kwak M, Toro O, Debouck DG, Gepts P. Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris). Ann Bot 2012; 110:1573-80. [PMID: 23019270 PMCID: PMC3503494 DOI: 10.1093/aob/mcs207] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/07/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS The actual number of domestications of a crop is one of the key questions in domestication studies. Answers to this question have generally been based on relationships between wild progenitors and domesticated descendants determined with anonymous molecular markers. In this study, this question was investigated by determining the number of instances a domestication phenotype had been selected in a crop species. One of the traits that appeared during domestication of common bean (Phaseolus vulgaris) is determinacy, in which stems end with a terminal inflorescence. It has been shown earlier that a homologue of the arabidopsis TFL1 gene - PvTFL1y - controls determinacy in a naturally occurring variation of common bean. METHODS Sequence variation was analysed for PvTFL1y in a sample of 46 wild and domesticated accessions that included determinate and indeterminate accessions. KEY RESULTS Indeterminate types - wild and domesticated - showed only synonymous nucleotide substitutions. Determinate types - observed only among domesticated accessions - showed, in addition to synonymous substitutions, non-synonymous substitutions, indels, a putative intron-splicing failure, a retrotransposon insertion and a deletion of the entire locus. The retrotransposon insertion was observed in 70 % of determinate cultivars, in the Americas and elsewhere. Other determinate mutants had a more restricted distribution in the Americas only, either in the Andean or in the Mesoamerican gene pool of common bean. CONCLUSIONS Although each of the determinacy haplotypes probably does not represent distinct domestication events, they are consistent with the multiple (seven) domestication pattern in the genus Phaseolus. The predominance of determinacy in the Andean gene pool may reflect domestication of common bean prior to maize introduction in the Andes.
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Affiliation(s)
- Myounghai Kwak
- Department of Plant Sciences/MS1, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, USA
| | - Orlando Toro
- Unidad de Recursos Genéticos, CIAT, Apartado Aéreo 6713, Cali, Colombia
| | - Daniel G. Debouck
- Unidad de Recursos Genéticos, CIAT, Apartado Aéreo 6713, Cali, Colombia
| | - Paul Gepts
- Department of Plant Sciences/MS1, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, USA
- For correspondence. E-mail
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Abstract
Phaseolin is the major seed storage protein of common bean (Phaseolus vulgaris L.). It is encoded by a small multigene family of 6-9 genes that are clustered in a single complex locus (Phs). We have constructed a long-range restriction map of the phaseolin genomic region, including the Phs locus and two flanking marker loci, D1861 and Bng060. Using a combination of high molecular weight DNA isolation, one- and two-dimensional pulsed-field gel electrophoresis of single and double restriction digests followed by Southern hybridization, and PCR analysis of individual fragments, we found that: (i) the maximum size of the Phs locus is 190 kb, (ii) the Phs locus may have increased in size during the evolution of P. vulgaris, (iii) the genomic region marked by D1861-Phs-Bng060 spans 5 cM, which corresponds to a maximum of 1.9 Mb, and (iv) the Phs locus could be oriented with respect to the two adjacent markers. Further progress in determining the gene arrangement in the Phs locus will require cloning and analysis of large DNA fragments containing phaseolin genes via BAC libraries. Key words : multigene family, physical distance, genome mapping, seed protein.
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Kouam EB, Pasquet RS, Campagne P, Tignegre JB, Thoen K, Gaudin R, Ouedraogo JT, Salifu AB, Muluvi GM, Gepts P. Genetic structure and mating system of wild cowpea populations in West Africa. BMC Plant Biol 2012; 12:113. [PMID: 22827925 PMCID: PMC3438136 DOI: 10.1186/1471-2229-12-113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 06/28/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cowpea is a highly inbred crop. It is part of a crop-weed complex, whose origin and dynamics is unknown, which is distributed across the African continent. This study examined outcrossing rates and genetic structures in 35 wild cowpea (Vigna unguiculata ssp. unguiculata var. spontanea) populations from West Africa, using 21 isozyme loci, 9 of them showing polymorphism. RESULTS Outcrossing rates ranged from 1% to 9.5% (mean 3.4%), which classifies the wild cowpea breeding system as primarily selfing, though rare outcrossing events were detected in each population studied. Furthermore, the analyses of both the genetic structure of populations and the relationships between the wild and domesticated groups suggest possibilities of gene flow that are corroborated by field observations. CONCLUSIONS As expected in a predominantly inbred breeding system, wild cowpea shows high levels of genetic differentiation and low levels of genetic diversity within populations. Gene flow from domesticated to wild cowpea does occur, although the lack of strong genetic swamping and modified seed morphology in the wild populations suggest that these introgressions should be rare.
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Affiliation(s)
- Eric B Kouam
- International Centre of Insect Physiology and Ecology, P.O box 30772, Nairobi, Kenya
- Department of Agriculture, Faculty of Agronomy and Agricultural Sciences, University of Dschang, PO Box 222, Dschang, Cameroon
| | - Remy S Pasquet
- International Centre of Insect Physiology and Ecology, P.O box 30772, Nairobi, Kenya
- IRD, Institut de Recherche pour le Développement, UR 072, Laboratoire Evolution, Génomes et Spéciation, UPR 9034, Centre National de la Recherche Scientifique (CNRS), 91198, Gif sur Yvette Cedex, France
- Université Paris-Sud 11, 91405, Orsay Cedex, France
| | - Pascal Campagne
- IRD, Institut de Recherche pour le Développement, UR 072, Laboratoire Evolution, Génomes et Spéciation, UPR 9034, Centre National de la Recherche Scientifique (CNRS), 91198, Gif sur Yvette Cedex, France
- Université Paris-Sud 11, 91405, Orsay Cedex, France
| | | | - Kevin Thoen
- International Centre of Insect Physiology and Ecology, P.O box 30772, Nairobi, Kenya
| | - Remi Gaudin
- Faculté des Sciences, Département de Biologie, BP 243, Niamey, Niger
- UMR System 2, place Viala, 34060, Montpellier, France
| | | | | | - Geoffrey M Muluvi
- Department of Biochemistry and Biotechnology, Kenyatta University, P.O Box 43844, Nairobi, Kenya
| | - Paul Gepts
- Department of Plant Sciences/MS1, Section of Crop and Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
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Repinski SL, Kwak M, Gepts P. The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1. Theor Appl Genet 2012; 124:1539-47. [PMID: 22331140 DOI: 10.1007/s00122-012-1808-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 01/26/2012] [Indexed: 05/18/2023]
Abstract
In a common bean plant exhibiting determinate growth, the terminal shoot meristem switches from a vegetative to reproductive state, resulting in a terminal inflorescence. Contrary to this, indeterminate growth habit results in a terminal meristem that remains vegetative where it further regulates the production of lateral vegetative and reproductive growth. In the last century, breeders have selected determinate growth habit, in combination with photoperiod insensitivity, to obtain varieties with a shorter flowering period, earlier maturation and ease of mechanized harvest. Previous work has identified TFL1 as a gene controlling determinate growth habit in Arabidopsis thaliana. In this work, we have validated that the Phaseolus vulgaris candidate gene, PvTFL1y, is the functional homolog of TFL1 using three independent lines of evidence. First, in a population of ~1,500 plants, PvTFL1y was found to co-segregate with the phenotypic locus for determinate growth habit (fin) on chromosome 01. Second, using quantitative PCR, we found that two unique haplotypes associated with determinacy at the PvTFL1y locus, a 4.1-kb retrotransposon and a splice-site mutation, cause mRNA abundance to decrease 20-133 fold, consistent with the recessive nature of fin. Finally, using a functional complementation approach, through Agrobacterium-mediated transformation of determinate Arabidopsis, we rescued tfl1-1 mutants with the wild-type PvTFL1y gene. Together, these three lines of evidence lead to the conclusion that PvTFL1y is the functional homolog of the Arabidopsis gene, TFL1, and is the gene responsible for naturally occurring variation for determinacy in common bean. Further work exploring the different haplotypes at the PvTFL1y locus may lead to improved plant architecture and phenology of common bean cultivars.
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Affiliation(s)
- S L Repinski
- Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA 95616-8780, USA
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Nanni L, Bitocchi E, Bellucci E, Rossi M, Rau D, Attene G, Gepts P, Papa R. Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.). Theor Appl Genet 2011; 123:1341-57. [PMID: 21830108 DOI: 10.1007/s00122-011-1671-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 07/26/2011] [Indexed: 05/19/2023]
Abstract
Evolutionary studies in plant and animal breeding are aimed at understanding the structure and organization of genetic variations of species. We have identified and characterized a genomic sequence in Phaseolus vulgaris of 1,200 bp (PvSHP1) that is homologous to SHATTERPROOF-1 (SHP1), a gene involved in control of fruit shattering in Arabidopsis thaliana. The PvSHP1 fragment was mapped to chromosome Pv06 in P. vulgaris and is linked to the flower and seed color gene V. Amplification of the PvSHP1 sequence from the most agronomically important legume species showed a high degree of interspecies diversity in the introns within the Phaseoleae, while the coding region was conserved across distant taxa. Sequencing of the PvSHP1 sequence in a sample of 91 wild and domesticated genotypes that span the geographic distribution of this species in the centers of origin showed that PvSHP1 is highly polymorphic and, therefore, particularly useful to further investigate the origin and domestication history of P. vulgaris. Our data confirm the gene pool structure seen in P. vulgaris along with independent domestication processes in the Andes and Mesoamerica; they provide additional evidence for a single domestication event in Mesoamerica. Moreover, our results support the Mesoamerican origin of this species. Finally, we have developed three indel-spanning markers that will be very useful for bean germplasm characterization, and particularly to trace the distribution of the domesticated Andean and Mesoamerican gene pools.
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Affiliation(s)
- L Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Alo F, Furman BJ, Akhunov E, Dvorak J, Gepts P. Leveraging genomic resources of model species for the assessment of diversity and phylogeny in wild and domesticated lentil. ACTA ACUST UNITED AC 2011; 102:315-29. [PMID: 21454287 DOI: 10.1093/jhered/esr015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Advances in comparative genomics have provided significant opportunities for analysis of genetic diversity in species with limited genomic resources, such as the genus Lens. Medicago truncatula expressed sequence tags (ESTs) were aligned with the Arabidopsis thaliana genome sequence to identify conserved exon sequences and splice sites in the ESTs. Conserved primers (CPs) based on M. truncatula EST sequences flanking one or more introns were then designed. A total of 22% of the CPs produced polymerase chain reaction amplicons in lentil and were used to sequence amplicons in 175 wild and 133 domesticated lentil accessions. Analysis of the sequences confirmed that L. nigricans and L. ervoides are well-defined species at the DNA sequence level. Lens culinaris subsp. odemensis, L. culinaris subsp. tomentosus, and L. lamottei may constitute a single taxon pending verification with crossability experiments. Lens culinaris subsp. orientalis is the progenitor of domesticated lentil, L. culinaris subsp. culinaris (as proposed before), but a more specific area of origin can be suggested in southern Turkey. We were also able to detect the divergence, following domestication, of the domesticated gene pool into overlapping large-seeded (megasperma) and small-seeded (microsperma) groups. Lentil domestication led to a loss of genetic diversity of approximately 40%. The approach followed in this research has allowed us to rapidly exploit sequence information from model plant species for the study of genetic diversity of a crop such as lentil with limited genomic resources.
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Affiliation(s)
- Fida Alo
- International Center for Agriculture in the Dry Areas, Aleppo, Syria
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