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Kumar K, Gupta P, Singh KN, Nirgude MS, Srivastava H, Sharma S, Sevanthi AM, Durgesh K, Jain PK, Gaikwad K. Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection. 3 Biotech 2023; 13:365. [PMID: 37840876 PMCID: PMC10575842 DOI: 10.1007/s13205-023-03785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03785-8.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh India
| | - Palak Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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2
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Catarcione G, Paolacci AR, Alicandri E, Gramiccia E, Taviani P, Rea R, Costanza MT, De Lorenzis G, Puccio G, Mercati F, Ciaffi M. Genetic Diversity and Population Structure of Common Bean ( Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:744. [PMID: 36840092 PMCID: PMC9968208 DOI: 10.3390/plants12040744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.
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Affiliation(s)
- Giulio Catarcione
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Anna Rita Paolacci
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Enrica Alicandri
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Elena Gramiccia
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | | | - Roberto Rea
- ARSIAL, Via Rodolfo Lanciani 38, 00162 Roma, Italy
| | | | | | | | | | - Mario Ciaffi
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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Cay SB, Cinar YU, Kuralay SC, Inal B, Zararsiz G, Ciftci A, Mollman R, Obut O, Eldem V, Bakir Y, Erol O. Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns. PLoS One 2022; 17:e0269747. [PMID: 35704623 PMCID: PMC9200356 DOI: 10.1371/journal.pone.0269747] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Crocus istanbulensis (B.Mathew) Rukšāns is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other Iridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.
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Affiliation(s)
- Selahattin Baris Cay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Yusuf Ulas Cinar
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Selim Can Kuralay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Behcet Inal
- Department of Agricultural Biotechnology, Faculty of Agriculture, University of Siirt, Siirt, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Almila Ciftci
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Rachel Mollman
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
- * E-mail:
| | - Yakup Bakir
- Department of Plant Bioactive Metabolites, ACTV Biotechnology, Inc., Istanbul, Turkey
| | - Osman Erol
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
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5
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Elias JCF, Gonçalves-Vidigal MC, Ariani A, Valentini G, Martiniano-Souza MDC, Vaz Bisneta M, Gepts P. Genome-Environment Association Analysis for Bio-Climatic Variables in Common Bean ( Phaseolus vulgaris L.) from Brazil. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081572. [PMID: 34451617 PMCID: PMC8399474 DOI: 10.3390/plants10081572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 05/08/2023]
Abstract
Abiotic stress is a limiting factor for common bean (Phaseolus vulgaris L.) production globally. The study of the genotypic, phenotypic, and bio-climatic variables in a broad set of accessions may assist the identification of genomic regions involved in the climatic adaptation of the common bean. We conducted a genotyping-by-sequencing analysis using 28,823 SNPs on 110 georeferenced common bean accessions from Brazil to discover associations between SNPs and bio-climatic indexes. The population structure analysis clustered the accessions into two groups corresponding to the Andean and Mesoamerican gene pools. Of the 19 bioclimatic variables, 17 exhibited a significant association with SNPs on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, Pv09, Pv10, and Pv11 of common bean. Ten candidate genes were associated with specific bio-climatic variables related to temperature and precipitation. The candidate genes associated with this significant Pv09 region encode a Platz transcription factor family protein previously reported to be an essential regulator of drought stress. The SNP markers and candidate genes associated with the bio-climatic variables should be validated in segregating populations for water stress, which could further be used for marker-assisted selection. As a result, bean breeding programs may be able to provide advances in obtaining drought-tolerant cultivars.
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Affiliation(s)
- Júlio Cesar F. Elias
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Maria Celeste Gonçalves-Vidigal
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
- Correspondence: ; Tel.:+55-449-9908-8186
| | | | - Giseli Valentini
- Soybean Genomics and Improvement Laboratory USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA;
| | - Maria da Conceição Martiniano-Souza
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95161-8780, USA;
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Chacón-Sánchez MI, Martínez-Castillo J, Duitama J, Debouck DG. Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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7
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Cortinovis G, Oppermann M, Neumann K, Graner A, Gioia T, Marsella M, Alseekh S, Fernie AR, Papa R, Bellucci E, Bitocchi E. Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean. Curr Protoc 2021; 1:e133. [PMID: 34004060 DOI: 10.1002/cpz1.133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The optimal use of legume genetic resources represents a key prerequisite for coping with current agriculture-related societal challenges, including conservation of agrobiodiversity, agricultural sustainability, food security, and human health. Among legumes, the common bean (Phaseolus vulgaris) is the most economically important for human consumption, and its evolutionary trajectories as a species have been crucial to determining the structure and level of its present and available genetic diversity. Genomic advances are considerably enhancing the characterization and assessment of important genetic variants. For this purpose, the development and availability of, and access to, well-described and efficiently managed genetic resource collections that comprise pure lines derived by single-seed-descent cycles will be paramount for the use of the reservoir of common bean variability and for the advanced breeding of legume crops. This is one of the main aims of the new and challenging European project INCREASE, which is the implementation of Intelligent Collections with appropriate standardized protocols that must be characterized, maintained, and made available, along with the related data, to users such as breeders and researchers. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterizing common bean seeds for seed trait descriptors Basic Protocol 2: Bean seed imaging Basic Protocol 3: Characterizing bean lines for plant trait descriptors specific for common bean Primary Seed Increase.
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Affiliation(s)
- Gaia Cortinovis
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Markus Oppermann
- Research Group Genebank Documentation, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Kerstin Neumann
- Research Group Genebank Documentation, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Graner
- Research Group Genebank Documentation, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), University of Basilicata, Potenza, Italy
| | - Marco Marsella
- International Treaty on Plant Genetic Resources for Food and Agriculture (FAO), Rome, Italy
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center for Plant Systems Biology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center for Plant Systems Biology, Plovdiv, Bulgaria
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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8
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Monteiro E, Castro I, Carvalho M, Martín JP, Rosa E, Carnide V. Iberian Peninsula cowpea diversity: chloroplast, microsatellite and morpho-agronomic variability. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1832155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Eliana Monteiro
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real 5000-801, Portugal
| | - Isaura Castro
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real 5000-801, Portugal
- Departamento de Genética e Biotecnologia, Escola de Ciências da Vida e do Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real 5000-801, Portugal
| | - Márcia Carvalho
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real 5000-801, Portugal
| | - Juan Pedro Martín
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, Madrid 28040, Spain
| | - Eduardo Rosa
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real 5000-801, Portugal
- Departamento de Agronomia, Escola de Ciências Agrárias e Veterinárias, Universidade de Trás-os-Montes e Alto Douro, Vila Real 5000-801, Portugal
| | - Valdemar Carnide
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real 5000-801, Portugal
- Departamento de Genética e Biotecnologia, Escola de Ciências da Vida e do Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real 5000-801, Portugal
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Tamburino R, Sannino L, Cafasso D, Cantarella C, Orrù L, Cardi T, Cozzolino S, D’Agostino N, Scotti N. Cultivated Tomato ( Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes. PLANTS 2020; 9:plants9111443. [PMID: 33114641 PMCID: PMC7692331 DOI: 10.3390/plants9111443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022]
Abstract
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy;
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Nunzio D’Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 133, 80055 Portici (NA), Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
- Correspondence: ; Tel.: +39-0812-53-9482
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10
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Fiore MC, Raimondo FM, Mercati F, Digangi I, Sunseri F, Scialabba A. Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection. PLANTS (BASEL, SWITZERLAND) 2020; 9:E989. [PMID: 32759817 PMCID: PMC7463873 DOI: 10.3390/plants9080989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/17/2022]
Abstract
The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the "Living Plants Germplasm Bank" at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the "Sicilian Plant Germplasm Repository" of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.
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Affiliation(s)
- Maria Carola Fiore
- Council for Agricultural Research and Economics Research Centre for Plant Protection and Certification (S.S. 113 km 245,500), 90011 Bagheria, Italy
| | | | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy;
| | - Ignazio Digangi
- Living Plants Germplasm Bank of Nebrodi, Contrada Pirato, 98060 Ucria (ME), Italy;
| | - Francesco Sunseri
- Department of Agraria, University Mediterranea of Reggio Calabria, Località Feo di Vito snc, 89124 Reggio Calabria, Italy;
| | - Anna Scialabba
- Department of Biological, Chemical and Pharmaceutical Science and Technologies (STEBICEF), University of Palermo, Via Archirafi 38, 90123 Palermo, Italy;
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11
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Long J, Zhang J, Zhang X, Wu J, Chen H, Wang P, Wang Q, Du C. Genetic Diversity of Common Bean ( Phaseolus vulgaris L.) Germplasm Resources in Chongqing, Evidenced by Morphological Characterization. Front Genet 2020; 11:697. [PMID: 32733540 PMCID: PMC7360827 DOI: 10.3389/fgene.2020.00697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/08/2020] [Indexed: 12/01/2022] Open
Abstract
In this study, the genetic diversity of 115 common bean germplasm resources collected from 27 counties in Chongqing over 3 years (2015–2017) was assessed. The results showed that the genetic diversity of the common bean germplasm resources was high, with an average diversity index of 1.447. The diversity of the qualitative traits of each organ was ranked as seed (H′ = 1.40) > pod (H′ = 1.062) > plant (H′ = 0.64) > leaf (H′ = 0.565), while the diversity of the quantitative traits of each organ was ranked as seed (H′ = 2.021) > pod (H′ = 1.989) > phenology (H′ = 1.941) > plant (H′ = 1.646). In the cluster analysis, 115 accessions were clustered into four groups. The accessions in the first and fourth group were characteristic of the Andean gene pool, while the accessions in the second group were characteristic of the Mesoamerican gene pool. However, the accessions of the third group possessed the combined characteristics of both gene pools and were thus classified as introgressed type. Four principal components represented 40.30% of the morphological diversity, with the first principal component representing the traits associated with plant growth; the second principal component representing flower characteristics; the third principal component being composed of seed characters; and the fourth principal component representing pod characteristics. The common bean germplasm resources are widely distributed in Chongqing, and the introgressed types are more prevalent in this region than elsewhere, with a rich genetic diversity and high utilization value in genetic breeding.
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Affiliation(s)
- Juechen Long
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Jijun Zhang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Xiaochun Zhang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Jing Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hong Chen
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Ping Wang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Qiang Wang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Chengzhang Du
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing, China
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12
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Cortinovis G, Frascarelli G, Di Vittori V, Papa R. Current State and Perspectives in Population Genomics of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2020; 9:E330. [PMID: 32150958 PMCID: PMC7154925 DOI: 10.3390/plants9030330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
* Correspondence: r [...].
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Affiliation(s)
| | | | | | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.C.); (G.F.); (V.D.V.)
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13
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. MICROBIOME 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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14
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Raatz B, Mukankusi C, Lobaton JD, Male A, Chisale V, Amsalu B, Fourie D, Mukamuhirwa F, Muimui K, Mutari B, Nchimbi-Msolla S, Nkalubo S, Tumsa K, Chirwa R, Maredia MK, He C. Analyses of African common bean ( Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding. GENETIC RESOURCES AND CROP EVOLUTION 2019; 66:707-722. [PMID: 30956400 PMCID: PMC6424151 DOI: 10.1007/s10722-019-00746-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/29/2019] [Indexed: 05/23/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.
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Affiliation(s)
- Bodo Raatz
- Present Address: Bean Program, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Clare Mukankusi
- International Centre for Tropical Agriculture (CIAT), 15 km Bombo Road, Kawanda, Box 6247, Kampala, Uganda
| | - Juan David Lobaton
- Present Address: Bean Program, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- School of Environmental and Rural Sciences, University of New England, Armidale, Australia
| | - Alan Male
- International Centre for Tropical Agriculture (CIAT), 15 km Bombo Road, Kawanda, Box 6247, Kampala, Uganda
| | - Virginia Chisale
- Chitedze Research Station, Department of Agricultural Research Services (DARS), P.O. Box 158, Lilongwe, Malawi
| | - Berhanu Amsalu
- Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research (EIAR), P.O. Box 436, Adama, Ethiopia
| | - Deidré Fourie
- ARC-Grain Crops Institute, Private Bag X1251, Potchefstroom, 2520 South Africa
| | | | - Kennedy Muimui
- Misamfu Regional Research Station, Zambia Agriculture Research Institute (ZARI), Box 410055, Kasama, Zambia
| | - Bruce Mutari
- Crop Breeding Institute, Department of Research and Specialist Services (DR&SS), Harare, Zimbabwe
| | | | - Stanley Nkalubo
- National Crops Resources Research Institute (NaCRRI)-Namulonge, P. O. Box 7084, Kampala, Uganda
| | - Kidane Tumsa
- Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research (EIAR), P.O. Box 436, Adama, Ethiopia
| | - Rowland Chirwa
- International Centre for Tropical Agriculture (CIAT), Mchinji Road, P.O. Box 158, Lilongwe, Malawi
| | | | - Chunlin He
- Genotyping Support Services (GSS), Generation Challenge Programme (GCP), c/o CIMMYT, Mexico, Mexico
- Present Address: Noble Research Institute, LLC, Ardmore, OK USA
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15
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Smýkal P, Hradilová I, Trněný O, Brus J, Rathore A, Bariotakis M, Das RR, Bhattacharyya D, Richards C, Coyne CJ, Pirintsos S. Genomic diversity and macroecology of the crop wild relatives of domesticated pea. Sci Rep 2017; 7:17384. [PMID: 29234080 PMCID: PMC5727218 DOI: 10.1038/s41598-017-17623-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/29/2017] [Indexed: 11/09/2022] Open
Abstract
There is growing interest in the conservation and utilization of crop wild relatives (CWR) in international food security policy and research. Legumes play an important role in human health, sustainable food production, global food security, and the resilience of current agricultural systems. Pea belongs to the ancient set of cultivated plants of the Near East domestication center and remains an important crop today. Based on genome-wide analysis, P. fulvum was identified as a well-supported species, while the diversity of wild P. sativum subsp. elatius was structured into 5 partly geographically positioned clusters. We explored the spatial and environmental patterns of two progenitor species of domesticated pea in the Mediterranean Basin and in the Fertile Crescent in relation to the past and current climate. This study revealed that isolation by distance does not explain the genetic structure of P. sativum subsp. elatius in its westward expansion from its center of origin. The genetic diversity of wild pea may be driven by Miocene-Pliocene events, while the phylogenetic diversity centers may reflect Pleisto-Holocene climatic changes. These findings help set research and discussion priorities and provide geographical and ecological information for germplasm-collecting missions, as well as for the preservation of extant diversity in ex-situ collections.
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Affiliation(s)
- Petr Smýkal
- Department of Botany, Palacký University in Olomouc, Olomouc, Czech Republic.
| | - Iveta Hradilová
- Department of Botany, Palacký University in Olomouc, Olomouc, Czech Republic
| | | | - Jan Brus
- Department of Geoinformatics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Abhishek Rathore
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Michael Bariotakis
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Roma Rani Das
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Christopher Richards
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, USA
| | - Clarice J Coyne
- United States Department of Agriculture, Washington State University, Pullman, Washington, USA
| | - Stergios Pirintsos
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
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16
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Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E, Ourari M, Aïnouche M, Salmon A, Cabello-Hurtado F, Aïnouche A. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res 2017; 24:343-358. [PMID: 28338826 PMCID: PMC5737547 DOI: 10.1093/dnares/dsx006] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/02/2017] [Indexed: 01/21/2023] Open
Abstract
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - M Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.,IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - G E Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
| | - J Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - J Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - E Coissac
- Laboratoire d'Ecologie Alpine, CNRS - Université de Grenoble 1 - Université de Savoie, 38041 Grenoble, France
| | - M Ourari
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie, Université Abderrahmane Mira, 06000 Bejaia, Algeria
| | - M Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
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17
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Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME JOURNAL 2017; 11:2244-2257. [PMID: 28585939 DOI: 10.1038/ismej.2017.85] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/23/2017] [Accepted: 04/14/2017] [Indexed: 01/04/2023]
Abstract
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.
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18
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Bitocchi E, Rau D, Bellucci E, Rodriguez M, Murgia ML, Gioia T, Santo D, Nanni L, Attene G, Papa R. Beans ( Phaseolus ssp.) as a Model for Understanding Crop Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:722. [PMID: 28533789 PMCID: PMC5420584 DOI: 10.3389/fpls.2017.00722] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Domenico Rau
- Department of Agriculture, University of SassariSassari, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | | | - Maria L. Murgia
- Department of Agriculture, University of SassariSassari, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of BasilicataPotenza, Italy
| | - Debora Santo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Giovanna Attene
- Department of Agriculture, University of SassariSassari, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
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19
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Bitocchi E, Rau D, Benazzo A, Bellucci E, Goretti D, Biagetti E, Panziera A, Laidò G, Rodriguez M, Gioia T, Attene G, McClean P, Lee RK, Jackson SA, Bertorelle G, Papa R. High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits. FRONTIERS IN PLANT SCIENCE 2017; 7:2005. [PMID: 28111584 PMCID: PMC5216878 DOI: 10.3389/fpls.2016.02005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/16/2016] [Indexed: 05/05/2023]
Abstract
Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of Phaseolus vulgaris by sequencing 49 gene fragments from a sample of 45 P. vulgaris wild and domesticated accessions, and as controls, two accessions each of the closely related species Phaseolus coccineus and Phaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Domenico Rau
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Daniela Goretti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå UniversityUmeå, Sweden
| | - Eleonora Biagetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Giovanni Laidò
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la CerealicolturaFoggia, Italy
| | - Monica Rodriguez
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della BasilicataPotenza, Italy
| | - Giovanna Attene
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Phillip McClean
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Rian K. Lee
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of GeorgiaAthens, GA, USA
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
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Mina-Vargas AM, McKeown PC, Flanagan NS, Debouck DG, Kilian A, Hodkinson TR, Spillane C. Origin of year-long bean (Phaseolus dumosus Macfady, Fabaceae) from reticulated hybridization events between multiple Phaseolus species. ANNALS OF BOTANY 2016; 118:957-969. [PMID: 27497241 PMCID: PMC5055819 DOI: 10.1093/aob/mcw138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/11/2016] [Accepted: 05/24/2016] [Indexed: 05/31/2023]
Abstract
Background and Aims Improved understanding of the secondary gene pools of crops is essential for advancing genetic gain in breeding programmes. Common bean, Phaseolus vulgaris, is a staple crop with several wild relatives in its secondary gene pool. The year-long bean, P. dumosus, an important crop in Guatemala, is considered particularly closely related to P. vulgaris and a potential source of novel variation. However, the genetic diversity and relationship to other Phaseolus species of P. dumosus remain unclear. Methods We conducted the first comprehensive investigation of P. dumosus genetic diversity using both nuclear and chloroplast genome markers. Our nuclear marker set included over 700 markers present within the Phaseolus DArT (Diversity Arrays Technology) array, which we applied to P. dumosus and other relatives of P. vulgaris (including every secondary gene pool species: P. acutifolius, P. albescens, P. coccineus and P. costaricensis). Key Results Phaseolus dumosus arose from hybridization of P. vulgaris and P. coccineus, followed by at least two later hybridizations with sympatric congener populations. Existing P. dumosus collections have low genetic diversity. Conclusions The under-utilized crop P. dumosus has a complex hybrid origin. Further sampling in the region in which it arose may uncover additional germplasm for introgressing favourable traits into crops within the P. vulgaris gene pool.
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Affiliation(s)
- Angela M. Mina-Vargas
- Genetics & Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Áras de Brún 2006, University Road, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter C. McKeown
- Genetics & Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Áras de Brún 2006, University Road, National University of Ireland Galway, Galway H91 REW4, Ireland
| | | | - Daniel G. Debouck
- International Center for Tropical Agriculture (CIAT), Apartado Aéreo 6713, Cali, Colombia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Building 3, Level D, University of Canberra, Kirinari Street, Bruce, ACT 2617, Australia
| | - Trevor R. Hodkinson
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Charles Spillane
- Genetics & Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Áras de Brún 2006, University Road, National University of Ireland Galway, Galway H91 REW4, Ireland
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21
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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. THE NEW PHYTOLOGIST 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] [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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22
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Curci PL, De Paola D, Sonnante G. Development of chloroplast genomic resources for Cynara. Mol Ecol Resour 2015; 16:562-73. [PMID: 26354522 DOI: 10.1111/1755-0998.12457] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/31/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.
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Affiliation(s)
- Pasquale L Curci
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
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23
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Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, Minio A, Rau D, Rodriguez M, Panziera A, Venturini L, Attene G, Albertini E, Jackson SA, Nanni L, Fernie AR, Nikoloski Z, Bertorelle G, Delledonne M, Papa R. Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. THE PLANT CELL 2014; 26:1901-1912. [PMID: 24850850 PMCID: PMC4079357 DOI: 10.1105/tpc.114.124040] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/15/2014] [Accepted: 04/29/2014] [Indexed: 05/02/2023]
Abstract
Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.
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Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Alberto Ferrarini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy
| | - Eleonora Biagetti
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Sebastian Klie
- Genes and Small Molecules Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Andrea Minio
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Domenico Rau
- Department of Agriculture, University of Sassari, 07100 Sassari, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, 07100 Sassari, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 S. Michele all'Adige, Italy
| | - Luca Venturini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Giovanna Attene
- Department of Agriculture, University of Sassari, 07100 Sassari, Italy
| | - Emidio Albertini
- Department of Applied Biology, University of Perugia, 06121 Perugia, Italy
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Laura Nanni
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy
| | | | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), 71122 Foggia, Italy
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24
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Goretti D, Bitocchi E, Bellucci E, Rodriguez M, Rau D, Gioia T, Attene G, McClean P, Nanni L, Papa R. Development of single nucleotide polymorphisms in Phaseolus vulgaris and related Phaseolus spp. MOLECULAR BREEDING 2014; 33:531-544. [PMID: 0 DOI: 10.1007/s11032-013-9970-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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25
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Pan L, Li Y, Guo R, Wu H, Hu Z, Chen C. Development of 12 chloroplast microsatellite markers in Vigna unguiculata (Fabaceae) and amplification in Phaseolus vulgaris. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1300075. [PMID: 25202608 PMCID: PMC4103102 DOI: 10.3732/apps.1300075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/05/2013] [Indexed: 05/26/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY Vigna unguiculata is an economically important legume, and the complexity of its variability and evolution needs to be further understood. Based on publicly available databases, we developed chloroplast microsatellite primers to investigate genetic diversity within V. unguiculata and its related species Phaseolus vulgaris. • METHODS AND RESULTS Twelve polymorphic chloroplast microsatellite markers were developed and characterized in 62 V. unguiculata individuals. The number of alleles per locus varied between two and four, the unbiased haploid diversity per locus ranged from 0.123 to 0.497, and the polymorphism information content varied from 0.114 to 0.369. In cross-species amplifications, nine of these markers showed polymorphism in 29 P. vulgaris individuals. • CONCLUSIONS The newly developed chloroplast microsatellite markers exhibit variation in V. unguiculata as well as their transferability in P. vulgaris. These markers can be used to investigate genetic diversity and evolution in V. unguiculata and P. vulgaris.
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Affiliation(s)
- Lei Pan
- School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
- Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
| | - Yi Li
- School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
- Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
| | - Rui Guo
- School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
- Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
| | - Hua Wu
- School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
- Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
| | - Zhihui Hu
- School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
- Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
| | - Chanyou Chen
- School of Life Sciences, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
- Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, Hubei, People’s Republic of China
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