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Pérez de los Cobos F, Coindre E, Dlalah N, Quilot-Turion B, Batlle I, Arús P, Eduardo I, Duval H. Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time. HORTICULTURE RESEARCH 2023; 10:uhad193. [PMID: 37927408 PMCID: PMC10623407 DOI: 10.1093/hr/uhad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023]
Abstract
Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | | | | | | | - Ignasi Batlle
- Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Abdulrahman SS, Daştan SD, Shahbaz SE, Selamoglu Z. Phylogenetic Analysis of Prunus Genus Using Nuclear and Chloroplast Gene Markers as a Bioorganic Structure Profiling. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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3
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Clavero-Camacho I, Cantalapiedra-Navarrete C, Archidona-Yuste A, Castillo P, Palomares-Rius JE. Distribution, Ecological Factors, Molecular Diversity, and Specific PCR for Major Species of Pin Nematodes ( Paratylenchus spp.) in Prunus Plantations in Spain. PLANT DISEASE 2022; 106:2711-2721. [PMID: 35259307 DOI: 10.1094/pdis-01-22-0188-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This study aimed to evaluate the prevalence and distribution of Paratylenchus species in the main areas of Prunus spp. production in Spain, their ecological constraints, and new molecular tools for the specific identification of major species. Pin nematodes are recognized as plant-parasitic nematodes with a wide host range and global distribution. Therefore, understanding the environmental and agronomic factors involved in their distribution is critical to design environmental and sustainable management strategies to reduce plant damage. A total of 219 sampling sites were surveyed and 12 Paratylenchus species were identified based on an integrative taxonomic approach (P. baldaccii, P. enigmaticus, P. goodeyi, P. hamatus, P. holdemani, P. indalus, P. israelensis, P. pedrami, P. tateae, P. tenuicaudatus, P. veruculatus, and P. zurgenerus). The most common pin nematode was P. hamatus, followed by P. tenuicaudatus. Nematode abundance was influenced by climatic characteristics, soil chemical properties, and agronomic management practices. Nine explanatory variables were selected as the most strongly associated with Paratylenchus distribution. Specifically, P. tenuicaudatus was significantly correlated with soil chemical characteristics, such as pH and carbon, sulfur, and sodium content, whereas P. goodeyi was closely related to fields with <10 years of almond cultivation. Species-specific PCRs were developed for P. hamatus and P. tenuicaudatus and their validity was evaluated studying the molecular variability of these species and against other Paratylenchus species.
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Affiliation(s)
- Ilenia Clavero-Camacho
- Institute for Sustainable Agriculture, Spanish National Research Council, 14004 Córdoba, Spain
| | | | - Antonio Archidona-Yuste
- Andalusian Institute of Agricultural and Fisheries Research and Training, 14004 Córdoba, Spain
| | - Pablo Castillo
- Institute for Sustainable Agriculture, Spanish National Research Council, 14004 Córdoba, Spain
| | - Juan E Palomares-Rius
- Institute for Sustainable Agriculture, Spanish National Research Council, 14004 Córdoba, Spain
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Hu G, Wu Y, Guo C, Lu D, Dong N, Chen B, Qiao Y, Zhang Y, Pan Q. Haplotype Analysis of Chloroplast Genomes for Jujube Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:841767. [PMID: 35360311 PMCID: PMC8961131 DOI: 10.3389/fpls.2022.841767] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/11/2022] [Indexed: 05/31/2023]
Abstract
Jujube (family Rhamnaceae) is an important economic fruit tree in China. In this study, we reported 26 chloroplast (cp) sequences of jujube using Illumina paired-end sequencing. The sequence length of cp genome was 161, 367-161, 849 bp, which was composed of a large single-copy region (89053-89437 bp) and a small single-copy region (19356-19362 bp) separated by a pair of reverse repeat regions (26478-26533 bp). Each cp genome encodes the same 130 genes, including 112 unique genes, being quite conserved in genome structure and gene sequence. A total of 118 single base substitutions (SNPs) and 130 InDels were detected in 65 jujube accessions. Phylogenetic and haplotype network construction methods were used to analyze the origin and evolution of jujube and its sour-tasting relatives. We detected 32 effective haplotypes, consisting of 20 unique jujube haplotypes and 9 unique sour-jujube haplotypes. Compared with sour-jujube, jujube showed greater haplotype diversity at the chloroplast DNA level. To cultivate crisp and sweet fruit varieties featuring strong resistance, by combining the characteristics of sour-jujube and cultivated jujube, three hybrid combinations were suggested for reciprocal crosses: "Dongzao" × "Jingzao39," "Dongzao" × "Jingzao60," "Dongzao" × "Jingzao28." This study provides the basis for jujube species' identification and breeding, and lays the foundation for future research.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuping Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qinghua Pan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Savoia MA, Del Faro L, Venerito P, Gaeta L, Palasciano M, Montemurro C, Sabetta W. The Relevance of Discovering and Recovering the Biodiversity of Apulian Almond Germplasm by Means of Molecular and Phenotypic Markers. PLANTS 2022; 11:plants11040574. [PMID: 35214907 PMCID: PMC8879738 DOI: 10.3390/plants11040574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/02/2022]
Abstract
Almond cultivation has great traditional and economic relevance in Southern Italy, especially in the Apulia region, where almond trees feature an ample and ancient varietal richness. To contrast the loss of plant genetic erosion and to safeguard the available bioresources, as well as to reinforce the local production, the regional Re.Ge.Fru.P. project aimed to re-evaluate, identify, and characterize the Apulian almond germplasm that is still uncharacterized and not jet studied using a dual (genetic and morphological) approach. Collection was conducted in the regional territory of 187 among the most widespread and minor or marginalized genotypes that were molecularly fingerprinted by means of 18 nuclear microsatellites (simple sequence repeats, SSRs). The high number of scored alleles reflected the great level of diversification within the Apulian germplasm, as also confirmed by neighbor joining and structure analysis, that clearly distinguished different genotype clusters. The phenotypic characterization using 17 morphological and phenological descriptors mirrored the genetic results, revealing a high degree of variability. The morphological traits with the best discriminatory ability were nut ventral suture, shell softness and shape and petal color. This work emphasizes the importance of recovering the genetic variability of Apulian almond germplasm, and the need to promote added value and enhance the local agri-food economy.
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Affiliation(s)
- Michele Antonio Savoia
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (M.A.S.); (M.P.); (C.M.)
| | - Loredana Del Faro
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy; (L.D.F.); (P.V.)
| | - Pasquale Venerito
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy; (L.D.F.); (P.V.)
| | - Liliana Gaeta
- Council for Agricultural Research and Economics-Agriculture and Environment Research Centre (CREA-AA), Via Celso Ulpiani 5, 70125 Bari, Italy;
| | - Marino Palasciano
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (M.A.S.); (M.P.); (C.M.)
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (M.A.S.); (M.P.); (C.M.)
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council (IPSP-CNR), Via Amendola 165/A, 70126 Bari, Italy
| | - Wilma Sabetta
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Via Amendola 165/A, 70126 Bari, Italy
- Correspondence:
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Tomishima H, Luo K, Mitchell AE. The Almond ( Prunus dulcis): Chemical Properties, Utilization, and Valorization of Coproducts. Annu Rev Food Sci Technol 2021; 13:145-166. [PMID: 34936815 DOI: 10.1146/annurev-food-052720-111942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Almonds (Prunus dulcis) are one of the most consumed tree-nuts worldwide, with commercial production in arid environments such as California, Spain, and Australia. The high consumption of almonds is partly due to their versatile usage in products such as gluten-free flour and dairy alternatives as well as them being a source of protein in vegetarian diets. They contain high concentrations of health-promoting compounds such as Vitamin E and have demonstrated benefits for reducing the risk of cardiovascular disease and improving vascular health. In addition, almonds are the least allergenic tree nut and contain minute quantities of cyanogenic glycosides. Production has increased significantly in the past two decades with 3.12 billion pounds of kernel meat produced in California alone in 2020 (USDA 2021), leading to a new emphasis on the valorization of the coproducts (e.g., hulls, shells, skins, and blanch water). This article presents a review of the chemical composition of almond kernels (e.g., macro and micronutrients, phenolic compounds, cyanogenic glycosides, and allergens) and the current research exploring the valorization of almond coproducts. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Haruka Tomishima
- Department of Food Science and Technology, University of California-Davis, Davis, California, USA;
| | - Kathleen Luo
- Department of Food Science and Technology, University of California-Davis, Davis, California, USA;
| | - Alyson E Mitchell
- Department of Food Science and Technology, University of California-Davis, Davis, California, USA;
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Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS). Genes (Basel) 2021; 12:genes12122007. [PMID: 34946959 PMCID: PMC8701156 DOI: 10.3390/genes12122007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.
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Pavan S, Delvento C, Mazzeo R, Ricciardi F, Losciale P, Gaeta L, D'Agostino N, Taranto F, Sánchez-Pérez R, Ricciardi L, Lotti C. Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight. HORTICULTURE RESEARCH 2021; 8:15. [PMID: 33423037 PMCID: PMC7797004 DOI: 10.1038/s41438-020-00447-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 05/04/2023]
Abstract
Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy.
- Institute of Biomedical Technologies, National Research Council (CNR), Via Amendola 122/D, Bari, 70126, Italy.
| | - Chiara Delvento
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Rosa Mazzeo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy
| | - Francesca Ricciardi
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy
| | - Pasquale Losciale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Liliana Gaeta
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment (CREA-AA), Bari, 70125, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, 80055, Italy
| | | | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy.
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Sánchez-Pérez R, Pavan S, Mazzeo R, Moldovan C, Aiese Cigliano R, Del Cueto J, Ricciardi F, Lotti C, Ricciardi L, Dicenta F, López-Marqués RL, Møller BL. Mutation of a bHLH transcription factor allowed almond domestication. Science 2020; 364:1095-1098. [PMID: 31197015 DOI: 10.1126/science.aav8197] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/23/2019] [Indexed: 11/02/2022]
Abstract
Wild almond species accumulate the bitter and toxic cyanogenic diglucoside amygdalin. Almond domestication was enabled by the selection of genotypes harboring sweet kernels. We report the completion of the almond reference genome. Map-based cloning using an F1 population segregating for kernel taste led to the identification of a 46-kilobase gene cluster encoding five basic helix-loop-helix transcription factors, bHLH1 to bHLH5. Functional characterization demonstrated that bHLH2 controls transcription of the P450 monooxygenase-encoding genes PdCYP79D16 and PdCYP71AN24, which are involved in the amygdalin biosynthetic pathway. A nonsynonymous point mutation (Leu to Phe) in the dimerization domain of bHLH2 prevents transcription of the two cytochrome P450 genes, resulting in the sweet kernel trait.
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Affiliation(s)
- R Sánchez-Pérez
- Department of Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Espinardo, Spain. .,Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - S Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro," 70126 Bari, Italy. .,Institute of Biomedical Technologies, National Research Council (CNR), 70126 Bari, Italy
| | - R Mazzeo
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,Department of Soil, Plant and Food Science, University of Bari "Aldo Moro," 70126 Bari, Italy
| | - C Moldovan
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - R Aiese Cigliano
- Sequentia Biotech SL, Campus de la UAB, 08193 Bellaterra, Barcelona, Spain
| | - J Del Cueto
- Department of Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Espinardo, Spain.,Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,Arboriculture Research Group, Agroscope, Conthey, Switzerland
| | - F Ricciardi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,Department of the Sciences of Agriculture, Food and Environment, University of Foggia, 71100 Foggia, Italy
| | - C Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, 71100 Foggia, Italy
| | - L Ricciardi
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro," 70126 Bari, Italy
| | - F Dicenta
- Department of Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Espinardo, Spain
| | - R L López-Marqués
- Transport Biology Section, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - B Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.,VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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Liu S, Cornille A, Decroocq S, Tricon D, Chague A, Eyquard JP, Liu WS, Giraud T, Decroocq V. The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events. Mol Ecol 2019; 28:5299-5314. [PMID: 31677192 DOI: 10.1111/mec.15296] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022]
Abstract
Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long-lived perennial fruit trees.
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Affiliation(s)
- Shuo Liu
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Yingkou City, China
| | - Amandine Cornille
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - David Tricon
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France
| | - Aurélie Chague
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France
| | | | | | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
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Xu W, Yang T, Qiu L, Chapman MA, Li D, Liu A. Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi-woody crop. PLANT DIRECT 2019; 3:e00173. [PMID: 31641699 PMCID: PMC6802463 DOI: 10.1002/pld3.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication origin, genomic variation, and potential targets of selection underlying domestication traits remain unknown. Here, we performed a phylogenetic analysis, which suggests that the wild accessions were distinctively separated from the cultivated accessions. Genome sequencing of three accessions (one each wild, landrace, and cultivar) showed a large number of genetic variants between wild and cultivated castor bean (ZB306 or Hale), and relatively few variants between cultivar ZB306 and Hale. Comparative genome analysis revealed many candidate genes of selection and key pathways potentially involved in the transition from a perennial woody tree to annual crop. Interestingly, among 16 oil-related genes only three showed evidence of selection and the remainder showed low genetic variation at the population level, suggesting strong purifying selection in both the wild and domesticated gene pools. These results extend our understanding of the origin, genomic variation, and domestication, and provide a valuable resource for future gene-trait associations and castor bean breeding.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Tianquan Yang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lijun Qiu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Mark A. Chapman
- Biological Sciences and Centre for Underutilised CropsUniversity of SouthamptonSouthamptonUK
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Aizhong Liu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of ChinaMinistry of EducationSouthwest Forestry UniversityKunmingChina
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Halász J, Kodad O, Galiba GM, Skola I, Ercisli S, Ledbetter CA, Hegedűs A. Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers. TREE GENETICS & GENOMES 2019; 15:12. [PMID: 0 DOI: 10.1007/s11295-019-1319-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/02/2019] [Accepted: 01/08/2019] [Indexed: 05/28/2023]
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14
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D'Agostino N, Taranto F, Camposeo S, Mangini G, Fanelli V, Gadaleta S, Miazzi MM, Pavan S, di Rienzo V, Sabetta W, Lombardo L, Zelasco S, Perri E, Lotti C, Ciani E, Montemurro C. GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars. Sci Rep 2018; 8:15877. [PMID: 30367101 PMCID: PMC6203791 DOI: 10.1038/s41598-018-34207-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/12/2018] [Indexed: 11/08/2022] Open
Abstract
Information on the distribution of genetic variation is essential to preserve olive germplasm from erosion and to recover alleles lost through selective breeding. In addition, knowledge on population structure and genotype-phenotype associations is crucial to support modern olive breeding programs that must respond to new environmental conditions imposed by climate change and novel biotic/abiotic stressors. To further our understanding of genetic variation in the olive, we performed genotype-by-sequencing on a panel of 94 Italian olive cultivars. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively. Both datasets were used to model population structure via parametric and non parametric clustering. Although the two pipelines yielded a 3-fold difference in the number of SNPs, both described wide genetic variability among our study panel and allowed individuals to be grouped based on fruit weight and the geographical area of cultivation. Multidimensional scaling analysis on identity-by-state allele-sharing values as well as inference of population mixtures from genome-wide allele frequency data corroborated the clustering pattern we observed. These findings allowed us to formulate hypotheses about geographical relationships of Italian olive cultivars and to confirm known and uncover novel cases of synonymy.
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Affiliation(s)
- Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano Faiano, Italy.
| | - Francesca Taranto
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy.
| | - Salvatore Camposeo
- Department of Agricultural and Environmental sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina Fanelli
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Susanna Gadaleta
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina di Rienzo
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Wilma Sabetta
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Luca Lombardo
- Center for Agriculture, Food ad Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Samanta Zelasco
- CREA Research Centre for Olive, Citrus and Tree Fruit, Rende, Italy
| | - Enzo Perri
- CREA Research Centre for Olive, Citrus and Tree Fruit, Rende, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Cinzia Montemurro
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
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Hamadeh B, Chalak L, Coppens d’Eeckenbrugge G, Benoit L, Joly HI. Evolution of almond genetic diversity and farmer practices in Lebanon: impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation. BMC PLANT BIOLOGY 2018; 18:155. [PMID: 30081821 PMCID: PMC6080396 DOI: 10.1186/s12870-018-1372-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 07/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Under cultivation, many outcrossing fruit tree species have switched from sexual reproduction to vegetative propagation. Traditional production systems have persisted, where cultivar propagation is based on a mixed reproductive system. For millenia, almond, Prunus dulcis, has been propagated by seeds. Almond grafting remained of little importance until recently. In Lebanon, both sexual and clonal reproductions are used for almond propagation. We used 15 microsatellite markers to investigate the effect of introducing graft-propagated cultivars and associated practices, on the structure of the genetic diversity among and within the two main Lebanese cultivars. RESULTS As expected, the sexually propagated cultivar Khachabi exhibited more genotypic and genetic diversity than the vegetatively propagated cultivar Halwani. It also exhibited lower differentiation among populations. The distribution of clones showed that propagation modes were not exclusive: farmers have introduced clonal propagation in the seed-propagated cultivar while they have maintained a diversity of genotypes within populations that were mostly graft-propagated. These practices are also important to avoid mate limitations that hamper fruit production in a self-incompatible species. 'Khachabi' is structured into two gene pools separated by the Lebanese mountains. As to 'Halwani', two different gene pools were introduced. The most ancient one shares the same geographic range as 'Khachabi'; longtime coexistence and sexual reproduction have resulted in admixture with 'Khachabi'. In contrast, the more recent introduction of the second gene pool in the Bekaa region followed an evolution towards more extensive clonal propagation of 'Halwani' limiting hybridizations. Furthermore, some pairs of geographically distant 'Halwani' orchards, exhibited low genetic distances, suggesting that a network of exchanges between farmers was effective on a large scale and/or that farmers brought clonal plant material from a common source. CONCLUSIONS Almond diversification in Lebanon is clearly related to the evolution of propagation practices adapted to self-incompatible cultivars. The comparison between both cultivars demonstrated the genetic effects of the introduction of a new cultivar and the associated grafting propagation practices. Our study provided information to develop a strategy for in situ conservation of cultivars and to limit gene flow from introduced material to ancient orchards.
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Affiliation(s)
- Bariaa Hamadeh
- Lebanese Agricultural Research Institute, Fanar, Lebanon
- Université Montpellier 2, UMR CEFE, 34293 Montpellier Cedex, France
- Doctoral School of Sciences and Technologies, Lebanese University, Hadath, Lebanon
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Lamis Chalak
- Faculty of Agriculture, Lebanese University, Dekwaneh, Lebanon
| | - Geo Coppens d’Eeckenbrugge
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Laure Benoit
- CIRAD, UMR CBGP, F-34398 Montpellier, France
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Hélène I. Joly
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Liu L, Wang Y, He P, Li P, Lee J, Soltis DE, Fu C. Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. BMC Genomics 2018; 19:235. [PMID: 29618324 PMCID: PMC5885378 DOI: 10.1186/s12864-018-4633-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4633-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yuewen Wang
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Peizi He
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, 34134, South Korea
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species. Sci Rep 2017; 7:5966. [PMID: 28729554 PMCID: PMC5519738 DOI: 10.1038/s41598-017-06084-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
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Liu LX, Li R, Worth JRP, Li X, Li P, Cameron KM, Fu CX. The Complete Chloroplast Genome of Chinese Bayberry ( Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales. FRONTIERS IN PLANT SCIENCE 2017; 8:968. [PMID: 28713393 PMCID: PMC5492642 DOI: 10.3389/fpls.2017.00968] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014-26,069 bp) separated by a large single-copy (LSC) region (88,683-88,809 bp) and a small single-copy (SSC) region (18,676-18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG, and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future research characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.
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Affiliation(s)
- Lu-Xian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan UniversityKaifeng, China
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Rui Li
- Food Inspection and Testing Institute of Henan ProvinceZhengzhou, China
| | - James R. P. Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research InstituteIbaraki, Japan
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
- *Correspondence: Pan Li,
| | | | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
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Abstract
The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
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21
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Dettori MT, Micali S, Giovinazzi J, Scalabrin S, Verde I, Cipriani G. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species. SPRINGERPLUS 2015; 4:337. [PMID: 26185739 PMCID: PMC4497997 DOI: 10.1186/s40064-015-1098-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/12/2015] [Indexed: 02/04/2023]
Abstract
A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10−7 in peach to 9.48 × 10−10 in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.
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Affiliation(s)
- Maria Teresa Dettori
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | - Sabrina Micali
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | - Jessica Giovinazzi
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | | | - Ignazio Verde
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | - Guido Cipriani
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
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22
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Rigoldi MP, Rapposelli E, De Giorgio D, Resta P, Porceddu A. Genetic diversity in two Italian almond collections. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2014.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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23
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Planas E, Saupe EE, Lima-Ribeiro MS, Peterson AT, Ribera C. Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin. BMC Evol Biol 2014; 14:195. [PMID: 25297820 PMCID: PMC4236462 DOI: 10.1186/s12862-014-0195-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity of the region, protracted human presence has obscured the biogeographic processes that shaped current diversity. Loxosceles rufescens (Araneae, Sicariidae) is an ideal example: native to the Mediterranean, the species has dispersed worldwide via cohabitation with humans. A previous study revealed considerable molecular diversity, suggesting cryptic species, but relationships among lineages did not correspond to geographic location. RESULTS Delimitation analyses on cytochrome c oxidase subunit I identified 11 different evolutionary lineages, presenting two contrasting phylogeographic patterns: (1) lineages with well-structured populations in Morocco and Iberia, and (2) lineages lacking geographic structure across the Mediterranean Basin. Dating analyses placed main diversification events in the Pleistocene, and multiple Pleistocene refugia, identified using ecological niche modeling (ENM), are compatible with allopatric differentiation of lineages. Human-mediated transportation appears to have complicated the current biogeography of this medically important and synanthropic spider. CONCLUSIONS We integrated ecological niche models with phylogeographic analyses to elucidate the evolutionary history of L. rufescens in the Mediterranean Basin, with emphasis on the origins of mtDNA diversity. We found support for the hypothesis that northern Africa was the center of origin for L. rufescens, and that current genetic diversity originated in allopatry, likely promoted by successive glaciations during the Pleistocene. We corroborated the scenario of multiple refugia within the Mediterranean, principally in northern Africa, combining results from eight atmosphere-ocean general circulation models (AOGCMs) with two different refugium-delimitation methodologies. ENM results were useful for providing general views of putative refugia, with fine-scale details depending on the level of stringency applied for agreement among models.
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Affiliation(s)
- Enric Planas
- Institut de Recerca de la Biodiversitat (IRBio), Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain.
| | - Erin E Saupe
- Department of Geology, University of Kansas, Lawrence, Kansas, USA. .,Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA.
| | - Matheus S Lima-Ribeiro
- Departamento de Ciências Biológicas, Universidade Federal de Goiás, Campus Jataí, Jataí, GO, Brasil.
| | | | - Carles Ribera
- Institut de Recerca de la Biodiversitat (IRBio), Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain.
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Qi XS, Yuan N, Comes HP, Sakaguchi S, Qiu YX. A strong 'filter' effect of the East China Sea land bridge for East Asia's temperate plant species: inferences from molecular phylogeography and ecological niche modelling of Platycrater arguta (Hydrangeaceae). BMC Evol Biol 2014; 14:41. [PMID: 24593236 PMCID: PMC4015774 DOI: 10.1186/1471-2148-14-41] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/25/2014] [Indexed: 11/27/2022] Open
Abstract
Background In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM). However, it is less clear when and how lineages diverged in this region, whether in full isolation or in the face of post-divergence gene flow. Here, we investigate the effects of Quaternary changes in climate and sea level on the evolutionary and demographic history of Platycrater arguta, a rare temperate understorey shrub with disjunct distributions in East China (var. sinensis) and South Japan (var. arguta). Molecular data were obtained from 14 P. arguta populations to infer current patterns of molecular structure and diversity in relation to past (Last Interglacial and Last Glacial Maximum) and present distributions based on ecological niche modelling (ENM). A coalescent-based isolation-with-migration (IM) model was used to estimate lineage divergence times and population demographic parameters. Results Combining information from nuclear/chloroplast sequence data with nuclear microsatellites, our IM analyses identify the two varieties as genetically distinct units that evolved in strict allopatry since the mid-Pleistocene, c. 0.89 (0.51–1.2) Ma. Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var. arguta post-glacial admixture. However, past species distribution modelling indicates that the species’ overall distribution has not greatly changed over the last glacial cycles. Conclusions Our findings highlight the important influence of ancient sea-level changes on the diversification of East Asia’s temperate flora. Implicitly, they challenge the notion of general temperate forest expansion across the ECS land bridge, demonstrating instead its ‘filter’ effect owing to an unsuitable environment for certain species and their biological (e.g., recruitment) properties.
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Affiliation(s)
| | | | | | | | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China.
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25
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Yuan JH, Cornille A, Giraud T, Cheng FY, Hu YH. Independent domestications of cultivated tree peonies from different wild peony species. Mol Ecol 2013; 23:82-95. [PMID: 24138195 DOI: 10.1111/mec.12567] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 11/30/2022]
Abstract
An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants.
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Affiliation(s)
- Jun-Hui Yuan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China; Landscape Architecture College, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
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26
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Besnard G, El Bakkali A, Haouane H, Baali-Cherif D, Moukhli A, Khadari B. Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture. ANNALS OF BOTANY 2013; 112:1293-302. [PMID: 24013386 PMCID: PMC3806528 DOI: 10.1093/aob/mct196] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The olive (Olea europaea subsp. europaea) was domesticated in the Mediterranean area but its wild relatives are distributed over three continents, from the Mediterranean basin to South Africa and south-western Asia. Recent studies suggested that this crop originated in the Levant while a secondary diversification occurred in most westward areas. A possible contribution of the Saharan subspecies (subsp. laperrinei) has been highlighted, but the data available were too limited to draw definite conclusions. Here, patterns of genetic differentiation in the Mediterranean and Saharan olives are analysed to test for recent admixture between these taxa. METHODS Nuclear microsatellite and plastid DNA (ptDNA) data were compiled from previous studies and completed for a sample of 470 cultivars, 390 wild Mediterranean trees and 270 Saharan olives. A network was reconstructed for the ptDNA haplotypes, while a Bayesian clustering method was applied to identify the main gene pools in the data set and then simulate and test for early generations of admixture between Mediterranean and Saharan olives. KEY RESULTS Four lineages of ptDNA haplotypes are recognized: three from the Mediterranean basin and one from the Sahara. Only one haplotype, primarily distributed in the Sahara, is shared between laperrinei and europaea. This haplotype is detected once in 'Dhokar', a cultivar from the Maghreb. Nuclear microsatellites show geographic patterns of genetic differentiation in the Mediterranean olive that reflect the primary origins of cultivars in the Levant, and indicate a high genetic differentiation between europaea and laperrinei. No first-generation hybrid between europaea and laperrinei is detected, but recent, reciprocal admixture between Mediterranean and Saharan subspecies is found in a few accessions, including 'Dhokar'. CONCLUSIONS This study reports for the first time admixture between Mediterranean and Saharan olives. Although its contribution remains limited, Laperrine's olive has been involved in the diversification of cultivated olives.
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Affiliation(s)
- G. Besnard
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062 Toulouse cedex 9, France
- For correspondance. E-mail
| | - A. El Bakkali
- INRA/CBNMed, UMR 1334, AGAP, 34060 Montpellier, France
- INRA, UR APCRPG, BP 578, Meknès, Morocco
| | - H. Haouane
- INRA/CBNMed, UMR 1334, AGAP, 34060 Montpellier, France
| | - D. Baali-Cherif
- BP44, Laboratoire de Recherche sur les Zones Arides, USTHB/INA, Alger, Algeria
| | - A. Moukhli
- INRA Marrakech, UR Amélioration des Plantes, Marrakech, Morocco
| | - B. Khadari
- INRA/CBNMed, UMR 1334, AGAP, 34060 Montpellier, France
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