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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. PLANTS (BASEL, SWITZERLAND) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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2
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Aleza P, Garavello MF, Rouiss H, Benedict AC, Garcia-Lor A, Hernández M, Navarro L, Ollitrault P. Inheritance pattern of tetraploids pummelo, mandarin, and their interspecific hybrid sour orange is highly influenced by their phylogenomic structure. FRONTIERS IN PLANT SCIENCE 2023; 14:1327872. [PMID: 38143579 PMCID: PMC10739408 DOI: 10.3389/fpls.2023.1327872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Citrus polyploidy is associated with a wide range of morphological, genetic, and physiological changes that are often advantageous for breeding. Citrus triploid hybrids are very interesting as new seedless varieties. However, tetraploid rootstocks promote adaptation to different abiotic stresses and promote resilience. Triploid and tetraploid hybrids can be obtained through sexual hybridizations using tetraploid parents (2x × 4x, 4x × 2x, or 4x × 4x), but more knowledge is needed about the inheritance pattern of tetraploid parents to optimize the efficiency of triploid varieties and tetraploid rootstock breeding strategies. In this work, we have analyzed the inheritance pattern of three tetraploid genotypes: 'Chandler' pummelo (Citrus maxima) and 'Cleopatra' mandarin (Citrus reticulata), which represent two clear examples of autotetraploid plants constituted by the genome of a single species, and the 'Sevillano' sour orange, which is an allotetraploid interspecific hybrid between C. maxima and C. reticulata. Polymorphic simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers were used to estimate parental heterozygosity restitution, and allele frequencies for centromeric loci were used to calculate the preferential pairing rate related to the proportion of disomic and tetrasomic segregation. The tetraploid pummelo and mandarin displayed tetrasomic segregation. Sour orange evidenced a clear intermediate inheritance for five of the nine chromosomes (1, 2, 5, 7, and 8), a slight tendency toward tetrasomic inheritance on chromosome 3, and intermediate inheritance with a tendency toward disomy for chromosomes 4, 6, and 9. These results indicate that the interspecific versus intraspecific phylogenomic origin affects preferential pairing and, therefore, the inheritance patterns. Despite its high level of heterozygosity, the important preferential chromosome pairing observed in sour orange results in a limited diversity of the genotypic variability of its diploid gametes, and consequently, a large part of the genetic value of the original diploid sour orange is transferred to the tetraploid progenies.
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Affiliation(s)
- Pablo Aleza
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Miguel Fernando Garavello
- Concordia Agricultural Experimental Station, National Agricultural Technology Institute, Concordia, Entre Ríos, Argentina
| | - Houssem Rouiss
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Ana Cristina Benedict
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Andres Garcia-Lor
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Maria Hernández
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Luis Navarro
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Patrick Ollitrault
- Centre de coopération internationale en recherche agronomique pour le développement Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (UMR AGAP) Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), INRAE, Institut Agro, Montpellier, France
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3
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Hua K, Li T, He Y, Guan A, Chen L, Gao Y, Xu Q, Wang H, Luo R, Zhao L, Jin H. Resistin secreted by porcine alveolar macrophages leads to endothelial cell dysfunction during Haemophilus parasuis infection. Virulence 2023; 14:2171636. [PMID: 36694280 PMCID: PMC9928480 DOI: 10.1080/21505594.2023.2171636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Haemophilus parasuis (H. parasuis) causes exudative inflammation, implying endothelial dysfunction during pathogen infection. However, so far, the molecular mechanism of endothelial dysfunction caused by H. parasuis has not been clarified. By using the transwell-based cell co-culture system, we demonstrate that knocking out resistin in porcine alveolar macrophages (PAMs) dramatically attenuated endothelial monolayer damage caused by H. parasuis. The resistin secreted by PAMs inhibited the expression of the tight junction proteins claudin-5 and occludin rather than the adherens junction protein VE-cadherin in co-cultured porcine aortic endothelial cells (PAECs). Furthermore, we demonstrate that resistin regulated claudin-5 and occludin expression and monolayer PAEC permeability in an LKB1/AMPK/mTOR pathway-dependent manner. Additionally, we reveal that the outer membrane lipoprotein gene lppA in H. parasuis induced resistin expression in PAMs, as deleting lppA reduced resistin expression in H. parasuis-infected PAMs, causing a significant change in LKB1/AMPK/mTOR pathway activity in co-cultured PAECs, thereby restoring tight junction protein levels and endothelial monolayer permeability. Thus, we postulate that the H. parasuis lppA gene enhances resistin production in PAMs, disrupting tight junctions in PAECs and causing endothelial barrier dysfunction. These findings elucidate the pathogenic mechanism of exudative inflammation caused by H. parasuis for the first time and provide a more profound angle of acute exudative inflammation caused by bacteria.
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Affiliation(s)
- Kexin Hua
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Tingting Li
- Department of Animal Disease Diagnosis, Hubei Animal Disease Prevention and Control Centre, Wuhan, China
| | - Yanling He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Aohan Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Liying Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Yuan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Qianshuan Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Haoyu Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, China,CONTACT Hui Jin
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Abderrahim KA, Remini H, Dahmoune F, Mouhoubi K, Berkani F, Abbou A, Aoun O, Dairi S, Belbahi A, Kadri N, Madani K. Influence of convective and microwave drying on Algerian blood orange slices: Drying kinetics and characteristics, modeling, and drying energetics. J FOOD PROCESS ENG 2022. [DOI: 10.1111/jfpe.14176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Khadidja Adel Abderrahim
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité (LGVRNAQ), Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
| | - Hocine Remini
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
| | - Farid Dahmoune
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
| | - Khokha Mouhoubi
- Centre de Recherche en Technologies Agro‐Alimentaires (CRTAA) Campus universitaire de Tergua Ouzemour Bejaia Algeria
| | - Farida Berkani
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité (LGVRNAQ), Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
| | - Amina Abbou
- Centre de Recherche en Technologies Agro‐Alimentaires (CRTAA) Campus universitaire de Tergua Ouzemour Bejaia Algeria
| | - Omar Aoun
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
- Département de Microbiologie et Biochimie, Faculté des Sciences Université de M'sila M'sila Algeria
| | - Sofiane Dairi
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
- Département de Microbiologie Appliquée et Sciences Alimentaires, Faculté des Sciences de la Nature et de la Vie Université de Jijel Jijel Algeria
| | - Amine Belbahi
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
- Département de Microbiologie et Biochimie, Faculté des Sciences Université de M'sila M'sila Algeria
| | - Nabil Kadri
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira Bouira Algeria
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
| | - Khodir Madani
- Laboratoire de Biochimie, Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie Université de Bejaia Bejaia Algeria
- Centre de Recherche en Technologies Agro‐Alimentaires (CRTAA) Campus universitaire de Tergua Ouzemour Bejaia Algeria
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5
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Breman FC, Chen G, Snijder RC, Schranz ME, Bakker FT. Repeatome-Based Phylogenetics in Pelargonium Section Ciconium (Sweet) Harvey. Genome Biol Evol 2021; 13:6454096. [PMID: 34893846 PMCID: PMC8684485 DOI: 10.1093/gbe/evab269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/23/2022] Open
Abstract
The repetitive part of the genome (the repeatome) contains a wealth of often overlooked information that can be used to resolve phylogenetic relationships and test evolutionary hypotheses for clades of related plant species such as Pelargonium. We have generated genome skimming data for 18 accessions of Pelargonium section Ciconium and one outgroup. We analyzed repeat abundancy and repeat similarity in order to construct repeat profiles and then used these for phylogenetic analyses. We found that phylogenetic trees based on read similarity were largely congruent with previous work based on morphological and chloroplast sequence data. For example, results agreed in identifying a “Core Ciconium” group which evolved after the split with P. elongatum. We found that this group was characterized by a unique set of repeats, which confirmed currently accepted phylogenetic hypotheses. We also found four species groups within P. sect. Ciconium that reinforce previous plastome-based reconstructions. A second repeat expansion was identified in a subclade which contained species that are considered to have dispersed from Southern Africa into Eastern Africa and the Arabian Peninsula. We speculate that the Core Ciconium repeat set correlates with a possible WGD event leading to this branch.
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Affiliation(s)
- Floris C Breman
- Biosystematics Group, Wageningen University & Research, Netherlands
| | - Guangnan Chen
- Biosystematics Group, Wageningen University & Research, Netherlands
| | | | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Netherlands
| | - Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Netherlands
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6
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Chemical Variability of Peel and Leaf Essential Oils in the Citrus Subgenus Papeda (Swingle) and Few Relatives. PLANTS 2021; 10:plants10061117. [PMID: 34073135 PMCID: PMC8227882 DOI: 10.3390/plants10061117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/03/2022]
Abstract
The Papeda Citrus subgenus includes several species belonging to two genetically distinct groups, containing mostly little-exploited wild forms of citrus. However, little is known about the potentially large and novel aromatic diversity contained in these wild citruses. In this study, we characterized and compared the essential oils obtained from peels and leaves from representatives of both Papeda groups, and three related hybrids. Using a combination of GC, GC-MS, and 13C-NMR spectrometry, we identified a total of 60 compounds in peel oils (PO), and 76 compounds in leaf oils (LO). Limonene was the major component in almost all citrus PO, except for C. micrantha and C. hystrix, where β-pinene dominated (around 35%). LO composition was more variable, with different major compounds among almost all samples, except for two citrus pairs: C. micrantha/C. hystrix and two accessions of C. ichangensis. In hybrid relatives, the profiles were largely consistent with their Citrus/Papeda parental lineage. This high chemical diversity, not only among the sections of the subgenus Papeda, but also between species and even at the intraspecific level, suggests that Papeda may be an important source of aroma diversity for future experimental crosses with field crop species.
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7
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Xu Y, Jia H, Wu X, Koltunow AM, Deng X, Xu Q. Regulation of nucellar embryony, a mode of sporophytic apomixis in Citrus resembling somatic embryogenesis. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101984. [PMID: 33418404 DOI: 10.1016/j.pbi.2020.101984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Apomixis, is an asexual mode of seed formation resulting in genetically identical or clonal seed with a maternal genotype. Apomixis has not been reported in seed crops where its flexible application in plant breeding could accelerate delivery of new varieties. By contrast, a sporophytic form of apomixis termed nucellar or adventitious embryony is common in the Rutaceae containing Citrus crop species. Here, multiple embryos develop from the maternal, somatic, nucellar cells of the ovule. They are incorporated into the enlarging embryo sac containing the sexually derived zygotic embryo and endosperm, which are products of double fertilization. Recent research has provided insights to the molecular basis for nucellar embryony. Here, we review the current understanding of the initiation, genetic basis and evolution of nucellar embryony in Citrus, and discuss prospects for future study and breeding applications of Citrus sporophytic apomixis.
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Affiliation(s)
- Yuantao Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Huihui Jia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Anna Mg Koltunow
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland, 4702, Australia.
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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8
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Mendes S, Régis T, Terol J, Soares Filho WDS, Talon M, Pedrosa-Harand A. Integration of mandarin ( Citrus reticulata) cytogenetic map with its genome sequence. Genome 2020; 63:437-444. [PMID: 32758104 DOI: 10.1139/gen-2020-0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Citrus is an extremely important genus in terms of world fruit production. Despite its economic importance and the small genome sizes of its species (2n = 18, 1C = 430 ± 68 Mbp), entire genomic assemblies have only recently become available for some of its representatives. Together with the previous CMA/DAPI banding and fluorescence in situ hybridization (FISH) in the group, these data are important for understanding the complex relationships between its species and for assisting breeding programs. To anchor genomic data with the cytogenetic map of mandarin (Citrus reticulata), the parental species of several economically important hybrids such as sweet orange and clementine, 18 BAC (bacterial artificial chromosome) clones were used. Eleven clementine BACs were positioned by BAC-FISH, doubling the number of chromosome markers so far available for BAC-FISH in citrus. Additionally, six previously mapped BACs were end-sequenced, allowing, together with one BAC previously sequenced, their assignment to scaffolds and the subsequent integration of chromosomes and the genome assembly. This study therefore established correlations between mandarin scaffolds and chromosomes, allowing further structural genomic and comparative study with the sweet orange genome, as well as insights into the chromosomal evolution of the group.
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Affiliation(s)
- Sandra Mendes
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Thallita Régis
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | | | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
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9
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Curtolo M, Granato LM, Soratto TAT, Curtolo M, Gazaffi R, Takita MA, Cristofani-Yaly M, Machado MA. Expression Quantitative Trait Loci (eQTL) mapping for callose synthases in intergeneric hybrids of Citrus challenged with the bacteria Candidatus Liberibacter asiaticus. Genet Mol Biol 2020; 43:e20190133. [PMID: 32568357 PMCID: PMC7295156 DOI: 10.1590/1678-4685-gmb-2019-0133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 01/07/2020] [Indexed: 11/21/2022] Open
Abstract
Citrus plants have been extremely affected by Huanglongbing (HLB) worldwide, causing
economic losses. HLB disease causes disorders in citrus plants, leading to callose
deposition in the phloem vessel sieve plates. Callose is synthesized by callose
synthases, which are encoded by 12 genes (calS1–
calS12)in Arabidopsis thaliana. We evaluated the
expression of eight callose synthase genes from Citrus in hybrids between
Citrus sunki and Poncirus trifoliata infected
with HLB. The objective of this work was to identify possible tolerance loci
combining the expression quantitative trait loci (eQTL) of different callose
synthases and genetic Single-Nucleotide Polymorphism (SNP) maps of C.
sunki and P. trifoliata. The expression data from all
CscalS ranged widely among the hybrids. Furthermore, the data
allowed the detection of 18 eQTL in the C. sunki map and 34 eQTL in
the P. trifoliata map. In both maps, some eQTL for different
CscalS were overlapped; thus, a single region could be associated
with the regulation of more than one CscalS. The regions identified
in this work can be interesting targets for future studies of Citrus
breeding programs to manipulate callose synthesis during HLB infection.
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Affiliation(s)
- Maiara Curtolo
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil.,Universidade Estadual de Campinas, Programa de Pós-Graduação em Genética e Biologia Molecular, Campinas, SP, Brazil
| | - Laís Moreira Granato
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Maisa Curtolo
- Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Programa de Pós-Graduação em Genética e Melhoramento de Plantas, Piracicaba, SP, Brazil
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos, Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Marcos Antonio Machado
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
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10
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Garavello M, Cuenca J, Garcia-Lor A, Ortega N, Navarro L, Ollitrault P, Aleza P. Male and female inheritance patterns in tetraploid 'Moncada' mandarin. PLANT CELL REPORTS 2020; 39:335-349. [PMID: 31781856 PMCID: PMC7018676 DOI: 10.1007/s00299-019-02494-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/20/2019] [Indexed: 05/11/2023]
Abstract
KEY MESSAGE Tetraploid `Moncada´ mandarin, used as male and female in interploidy hybridizations, displays mainly tetrasomic inheritance for most LGs, with slight variations according to the direction of the crossing. Triploid-breeding programs in citrus are key tool to develop seedless cultivars. Obtaining triploid citrus hybrids may be achieved through different strategies, such as the exploitation of female unreduced gamete in crosses between diploid parents and diploid by tetraploid sexual hybridizations, in which tetraploid genotypes can be used as male or female parents. Genetic configuration of triploid populations from interploid crosses greatly depends on the chromosomic segregation mode of the tetraploid parent used. Here, we have analyzed the inheritance of the tetraploid 'Moncada' mandarin and compared the genetic structures of the resulting gametes when used as male and as female parent. The preferential chromosome pairing rate is calculated from the parental heterozygosity restitution (PHR) of codominant molecular markers, indicating the proportion between disomic and tetrasomic segregation. Tetraploid 'Moncada' both as female and male parent largely exhibited tetrasomic segregation. However, as female parent, one linkage group (LG8) showed intermediate segregation with tendency towards tetrasomic inheritance, while another linkage group (LG4) evidenced a clear intermediate segregation. On the other hand, when used as male parent two linkage groups (LG5 and LG6) showed values that fit an intermediate inheritance model with tetrasomic tendency. Significant doubled reduction (DR) rates were observed in five linkage groups as female parent, and in six linkage groups as male parent. The new knowledge generated here will serve to define crossing strategies in citrus improvement programs to efficiently obtain new varieties of interest in the global fresh consumption market.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
- INTA, Concordia Agricultural Experiment Station, 3200, Concordia, CC 34, Entre Ríos, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Andrés Garcia-Lor
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Neus Ortega
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Patrick Ollitrault
- Unité Mixte de Recherche, Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Corse, 20230, San Giuliano, France.
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain.
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11
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Garavello M, Cuenca J, Dreissig S, Fuchs J, Navarro L, Houben A, Aleza P. Analysis of Crossover Events and Allele Segregation Distortion in Interspecific Citrus Hybrids by Single Pollen Genotyping. FRONTIERS IN PLANT SCIENCE 2020; 11:615. [PMID: 32523591 PMCID: PMC7261893 DOI: 10.3389/fpls.2020.00615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/21/2020] [Indexed: 05/17/2023]
Abstract
In citrus, a classical method of studying crossovers and segregation distortion (SD) is the genetic analysis of progenies. A new strategy combining fluorescence-activated cell sorting and whole genome amplification of haploid pollen nuclei with a large set of molecular markers, offers the opportunity to efficiently determine the frequency of crossovers and the identification of SD without the need to generate segregating populations. Here we have analyzed meiotic crossover events in a pollen nuclei population from "Eureka" lemon and the allelic SD was evaluated in a pollen nuclei population from a clementine × sweet orange hybrid ("CSO"). Data obtained from the "CSO" pollen nuclei population were compared to those obtained from genotyping of a segregating population ("RTSO") arising from a hand-made sexual hybridization between diploid non apomictic selected tangor (mandarin × sweet orange; "RTO" tangor) as female parent pollinated with "CSO" tangor as male parent. The analysis of crossovers rates on chromosome 1 revealed the presence of up to five crossovers events on one arm and four on the corresponding other arm, with an average of 1.97 crossovers per chromosome while no crossover events were observed in five "Eureka" lemon pollen nuclei. The rate of SD observed in "CSO" pollen nuclei (13.8%) was slightly lower than that recovered in the "RTSO" population (20.7%). In the pollen nuclei population, SD was found on linkage group (LG) 2, while the "RTSO" population showed SD on LGs 2 and 7. Potential male gametic selection mechanisms were distinguished in pollen grains, while in the population, mechanisms of gametophytic selection and/or zygotic selection were observed. This methodology is a very useful tool to facilitate research focused on the reproductive biology of citrus and study the mechanisms that affect crossovers and SD.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- Concordia Agricultural Experiment Station, National Agricultural Technology Institute, Entre Ríos, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- *Correspondence: Pablo Aleza,
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12
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Zhong G, Nicolosi E. Citrus Origin, Diffusion, and Economic Importance. COMPENDIUM OF PLANT GENOMES 2020. [DOI: 10.1007/978-3-030-15308-3_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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do Amaral M, Barbosa de Paula MF, Ollitrault F, Rivallan R, de Andrade Silva EM, da Silva Gesteira A, Luro F, Garcia D, Ollitrault P, Micheli F. Phylogenetic Origin of Primary and Secondary Metabolic Pathway Genes Revealed by C. maxima and C. reticulata Diagnostic SNPs. FRONTIERS IN PLANT SCIENCE 2019; 10:1128. [PMID: 31608086 PMCID: PMC6771394 DOI: 10.3389/fpls.2019.01128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Modern cultivated Citrus species and varieties result from interspecific hybridization between four ancestral taxa. Among them, Citrus maxima and Citrus reticulata, closely associated with the pummelo and mandarin horticultural groups, respectively, were particularly important as the progenitors of sour and sweet oranges (Citrus aurantium and Citrus sinensis), grapefruits (Citrus paradisi), and hybrid types resulting from modern breeding programs (tangors, tangelos, and orangelos). The differentiation between the four ancestral taxa and the phylogenomic structure of modern varieties widely drive the phenotypic diversity's organization. In particular, strong phenotypic differences exist in the coloration and sweetness and represent important criteria for breeders. In this context, focusing on the genes of the sugar, carotenoid, and chlorophyll biosynthesis pathways, the aim of this work was to develop a set of diagnostic single-nucleotide polymorphism (SNP) markers to distinguish the ancestral haplotypes of C. maxima and C. reticulata and to provide information at the intraspecific diversity level (within C. reticulata or C. maxima). In silico analysis allowed the identification of 3,347 SNPs from selected genes. Among them, 1,024 were detected as potential differentiation markers between C. reticulata and C. maxima. A total of 115 SNPs were successfully developed using a competitive PCR technology. Their transferability among all Citrus species and the true citrus genera was very good, with only 0.87% of missing data. The ancestral alleles of the SNPs were identified, and we validated the usefulness of the developed markers for tracing the ancestral haplotype in large germplasm collections and sexually recombined progeny issued from the C. reticulata/C. maxima admixture gene pool. These markers will pave the way for targeted association studies based on ancestral haplotypes.
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Affiliation(s)
- Milena do Amaral
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Marcia Fabiana Barbosa de Paula
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | | | | | - Edson Mario de Andrade Silva
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | | | | | | | | | - Fabienne Micheli
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
- CIRAD, UMR AGAP, Montpellier, France
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Moonsap P, Laksanavilat N, Sinumporn S, Tasanasuwan P, Kate-Ngam S, Jantasuriyarat C. Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers. J Genet 2019; 98:80. [PMID: 31544784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice is believed to have originated from Indo-China, area between China and India, and then spread throughout the world. The Indochina region mainly includes countries like Thailand, Laos and Vietnam, which are the world's major rice exporters. Rice varieties grown in this area are highly diverse due to their different environment, ecosystem and climatic conditions. The objective of this study was to evaluate the genetic relationship of Indochina rice varieties using intersimple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP) and insertion-deletion (InDel) markers. Forty-six rice varieties, including 16, 4,11 and 15 from Thailand, China, Laos and Vietnam, respectively were used in this study. Seventeen of the 20 ISSR primers showed 82.96% polymorphism. At the same time, 17 of the 30 primer pairs of SRAP marker showed clear DNA amplification, which resulted in 84.79% polymorphism. Ninety-seven of 133 InDel markers have about 99.47% polymorphism. Three markers showed average PIC score ranging from 0.20 to 0.26. When the analysis was conducted using UPGMA clustering method, it was found that the combined data from three markers gave a better result than each marker separately. The results from clustering analysis showed that all accessions can be grouped based on their location and can be categorized into two major groups. Useful results from this study could bring substantial benefits and ultimately help the rice breeders to develop elite rice varieties in future.
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Affiliation(s)
- Pattaraborn Moonsap
- Faculty of Science, Department of Genetics, Kasetsart University, 50 Ngam, Wong Wan Rd., Ladyaw, Chatuchak, Bangkok 10900, Thailand.
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15
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16
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Ahmed D, Comte A, Curk F, Costantino G, Luro F, Dereeper A, Mournet P, Froelicher Y, Ollitrault P. Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus. ANNALS OF BOTANY 2019; 123:1231-1251. [PMID: 30924905 PMCID: PMC6612944 DOI: 10.1093/aob/mcz029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 02/18/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Reticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly to be used for large populations. The aim of this work was to develop an approach to infer phylogenomic structures in diploid, triploid and tetraploid individuals from sequencing data in reduced genome complexity libraries. The approach was applied to the cultivated Citrus gene pool resulting from reticulate evolution involving four ancestral taxa, C. maxima, C. medica, C. micrantha and C. reticulata. METHODS A genotyping by sequencing library was established with the restriction enzyme ApeKI applying one base (A) selection. Diagnostic single nucleotide polymorphisms (DSNPs) for the four ancestral taxa were mined in 29 representative varieties. A generic pipeline based on a maximum likelihood analysis of the number of read data was established to infer ancestral contributions along the genome of diploid, triploid and tetraploid individuals. The pipeline was applied to 48 diploid, four triploid and one tetraploid citrus accessions. KEY RESULTS Among 43 598 mined SNPs, we identified a set of 15 946 DSNPs covering the whole genome with a distribution similar to that of gene sequences. The set efficiently inferred the phylogenomic karyotype of the 53 analysed accessions, providing patterns for common accessions very close to that previously established using WGS data. The complex phylogenomic karyotypes of 21 cultivated citrus, including bergamot, triploid and tetraploid limes, were revealed for the first time. CONCLUSIONS The pipeline, available online, efficiently inferred the phylogenomic structures of diploid, triploid and tetraploid citrus. It will be useful for any species whose reproductive behaviour resulted in an interspecific mosaic of large genomic fragments. It can also be used for the first generations of interspecific breeding schemes.
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Affiliation(s)
- Dalel Ahmed
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - Aurore Comte
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Franck Curk
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gilles Costantino
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - François Luro
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - Alexis Dereeper
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Pierre Mournet
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | - Yann Froelicher
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, San Giuliano, France
| | - Patrick Ollitrault
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, San Giuliano, France
- For correspondence. E-mail
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17
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Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC Genomics 2019; 20:331. [PMID: 31046664 PMCID: PMC6498479 DOI: 10.1186/s12864-019-5712-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus. Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Montanari
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Nahla V Bassil
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Joseph Postman
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Biff Kitson
- Motueka Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Motueka, New Zealand
| | - Cecilia H Deng
- Auckland Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Kate Evans
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, USA
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Huang M, Roose ML, Yu Q, Du D, Yu Y, Zhang Y, Deng Z, Stover E, Gmitter FG. Construction of High-Density Genetic Maps and Detection of QTLs Associated With Huanglongbing Tolerance in Citrus. FRONTIERS IN PLANT SCIENCE 2018; 9:1694. [PMID: 30542355 PMCID: PMC6278636 DOI: 10.3389/fpls.2018.01694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/31/2018] [Indexed: 05/29/2023]
Abstract
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (Citrus sinensis) are highly susceptible to HLB, and trifoliate orange (Poncirus trifoliata, a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F1 population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F1 population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18-30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.
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Affiliation(s)
- Ming Huang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Qibin Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Dongliang Du
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yuan Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yi Zhang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Zhanao Deng
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Ed Stover
- United States Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Fort Pierce, FL, United States
| | - Frederick G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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Ruiz M, Pensabene-Bellavia G, Quiñones A, García-Lor A, Morillon R, Ollitrault P, Primo-Millo E, Navarro L, Aleza P. Molecular Characterization and Stress Tolerance Evaluation of New Allotetraploid Somatic Hybrids Between Carrizo Citrange and Citrus macrophylla W. rootstocks. FRONTIERS IN PLANT SCIENCE 2018; 9:901. [PMID: 30123223 PMCID: PMC6085489 DOI: 10.3389/fpls.2018.00901] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/07/2018] [Indexed: 05/18/2023]
Abstract
Polyploidy is one of the main forces that drives the evolution of plants and provides great advantages for breeding. Somatic hybridization by protoplast fusion is used in citrus breeding programs. This method allows combining the whole parental genomes in a single genotype, adding complementary dominant characters, regardless of parental heterozygosity. It also contributes to surpass limitations imposed by reproductive biology and quickly generates progenies that combine the required traits. Two allotetraploid somatic hybrids recovered from the citrus rootstocks-Citrus macrophylla (CM) and Carrizo citrange (CC)-were characterized for morphology, genome composition using molecular markers (SNP, SSR, and InDel), and their tolerance to iron chlorosis, salinity, and Citrus tristeza virus (CTV). Both hybrids combine the whole parental genomes even though the loss of parental alleles was detected in most linkage groups. Mitochondrial genome was inherited from CM in both the hybrids, whereas recombination was observed for chloroplastic genome. Thus, somatic hybrids differ from each other in their genome composition, indicating that losses and rearrangements occurred during the fusion process. Both inherited the tolerance to stem pitting caused by CTV from CC, are tolerant to iron chlorosis such as CM, and have a higher tolerance to salinity than the sensitive CC. These hybrids have potential as improved rootstocks to grow citrus in areas with calcareous and saline soils where CTV is present, such as the Mediterranean region. The provided knowledge on the effects of somatic hybridization on the genome composition, anatomy, and physiology of citrus rootstocks will be key for breeding programs that aim to address current and future needs of the citrus industry.
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Affiliation(s)
- Marta Ruiz
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Giovanni Pensabene-Bellavia
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Ana Quiñones
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Andrés García-Lor
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Raphaël Morillon
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Montpellier, France
| | - Patrick Ollitrault
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Montpellier, France
| | - Eduardo Primo-Millo
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
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Rouiss H, Bakry F, Froelicher Y, Navarro L, Aleza P, Ollitrault P. Origin of C. latifolia and C. aurantiifolia triploid limes: the preferential disomic inheritance of doubled-diploid 'Mexican' lime is consistent with an interploid hybridization hypothesis. ANNALS OF BOTANY 2018; 121:571-585. [PMID: 29293884 PMCID: PMC5838810 DOI: 10.1093/aob/mcx179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/14/2017] [Indexed: 05/23/2023]
Abstract
Background and Aims Two main types of triploid limes are produced worldwide. The 'Tahiti' lime type (Citrus latifolia) is predominant, while the 'Tanepao' type (C. aurantiifolia) is produced to a lesser extent. Both types result from natural interspecific hybridization involving a diploid gamete of C. aurantiifolia 'Mexican' lime type (itself a direct interspecific C. micrantha × C. medica hybrid). The meiotic behaviour of a doubled-diploid 'Mexican' lime, the interspecific micrantha/medica recombination and the resulting diploid gamete structures were analysed to investigate the possibility that 'Tahiti' and 'Tanepao' varieties are derived from natural interploid hybridization. Methods A population of 85 tetraploid hybrids was established between a doubled-diploid clementine and a doubled-diploid 'Mexican' lime and used to infer the genotypes of 'Mexican' lime diploid gametes. Meiotic behaviour was studied through combined segregation analysis of 35 simple sequenbce repeat (SSR) and single nucleotide polymorphismn (SNP) markers covering the nine citrus chromosomes and cytogenetic studies. It was supplemented by pollen viability assessment. Key Results Pollen viability of the doubled-diploid Mexican lime (64 %) was much higher than that of the diploid. On average, 65 % of the chromosomes paired as bivalents and 31.4 % as tetravalents. Parental heterozygosity restitution ranged from 83 to 99 %. Disomic inheritance with high preferential pairing values was deduced for three chromosomes. Intermediate inheritances, with disomic trend, were found for five chromosomes, and an intermediate inheritance was observed for one chromosome. The average effective interspecific recombination rate was low (1.2 cM Mb-1). Conclusion The doubled-diploid 'Mexican' lime had predominantly disomic segregation, producing interspecific diploid gamete structures with high C. medica/C. micrantha heterozygosity, compatible with the phylogenomic structures of triploid C. latifolia and C. aurantiifolia varieties. This disomic trend limits effective interspecific recombination and diversity of the diploid gamete population. Interploid reconstruction breeding using doubled-diploid lime as one parent is a promising approach for triploid lime diversification.
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Affiliation(s)
- H Rouiss
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe, France
| | - F Bakry
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Y Froelicher
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San Giuliano, Corse, France
| | - L Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - P Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - P Ollitrault
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe, France
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21
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Goldenberg L, Yaniv Y, Porat R, Carmi N. Mandarin fruit quality: a review. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018. [PMID: 28631804 DOI: 10.1002/jsfa.8495] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
During the last decade, there has been a continuous rise in consumption and global marketing of fresh, easy-to-peel mandarins, with current annual production of nearly 29 million tons. Nevertheless, most of the existing knowledge on quality traits of citrus fruit comes from research conducted on oranges and grapefruit, which are the main products for the citrus juice manufacturing industry; relatively little is yet known regarding the unique fruit quality traits of mandarins, nor about the great diversity in these traits among the various natural sub-groups and varieties of mandarins. In the present review we discuss the physiological, biochemical, and molecular factors governing key fruit quality attributes of mandarins, including fruit colour, size and shape, ease of peeling, seedlessness, flavour, and nutritional quality. Fruit colour, size, and shape contribute to external appearance; peelability and seedlessness to ease of consumption; and flavour and nutritional quality to internal quality. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Livnat Goldenberg
- Department of Postharvest Science of Fresh Produce, ARO, the Volcani Center, Bet Dagan, Israel
- Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel
| | - Yossi Yaniv
- Department of Fruit Tree Crops, ARO, the Volcani Center, Bet Dagan, Israel
| | - Ron Porat
- Department of Postharvest Science of Fresh Produce, ARO, the Volcani Center, Bet Dagan, Israel
| | - Nir Carmi
- Department of Fruit Tree Crops, ARO, the Volcani Center, Bet Dagan, Israel
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22
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Huang M, Roose ML, Yu Q, Du D, Yu Y, Zhang Y, Deng Z, Stover E, Gmitter FG. Construction of High-Density Genetic Maps and Detection of QTLs Associated With Huanglongbing Tolerance in Citrus. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30542355 DOI: 10.1101/330753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (Citrus sinensis) are highly susceptible to HLB, and trifoliate orange (Poncirus trifoliata, a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F1 population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F1 population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18-30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.
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Affiliation(s)
- Ming Huang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Qibin Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Dongliang Du
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yuan Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yi Zhang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Zhanao Deng
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Ed Stover
- United States Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Fort Pierce, FL, United States
| | - Frederick G Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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23
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Oueslati A, Salhi-Hannachi A, Luro F, Vignes H, Mournet P, Ollitrault P. Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits. PLoS One 2017; 12:e0185618. [PMID: 28982157 PMCID: PMC5628881 DOI: 10.1371/journal.pone.0185618] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the "small citrus" modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the "phylogenomic karyotypes" of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics.
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Affiliation(s)
- Amel Oueslati
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Tunis, Tunisia
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement Petit-Bourg, Guadeloupe, France
| | - Amel Salhi-Hannachi
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Tunis, Tunisia
| | - François Luro
- AGAPResearch Unit, Institut National de la Recherche Agronomique, San Giuliano, France
| | - Hélène Vignes
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Pierre Mournet
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Patrick Ollitrault
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement Petit-Bourg, Guadeloupe, France
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24
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Rouiss H, Cuenca J, Navarro L, Ollitrault P, Aleza P. Unreduced Megagametophyte Production in Lemon Occurs via Three Meiotic Mechanisms, Predominantly Second-Division Restitution. FRONTIERS IN PLANT SCIENCE 2017; 8:1211. [PMID: 28747921 PMCID: PMC5506204 DOI: 10.3389/fpls.2017.01211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/27/2017] [Indexed: 05/23/2023]
Abstract
Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, "Eureka Frost" and "Fino", using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation. We utilized a maximum-likelihood method based on parental heterozygosity restitution (PHR) of centromeric markers and analysis of PHR patterns along the chromosome. The frequency of 2n gamete production was 4.9% for "Eureka Frost" and 8.3% for "Fino", with three meiotic mechanisms leading to 2n gamete formation. We performed the maximum-likelihood method at the individual level via centromeric marker analysis, finding that 88% of the hybrids arose from second-division restitution (SDR), 7% from first-division restitution (FDR) or pre-meiotic doubling (PRD), and 5% from post-meiotic genome doubling (PMD). The pattern of PHR along LG1 confirmed that SDR is the main mechanism for 2n gamete production. Recombination analysis between markers in this LG revealed partial chiasma interference on both arms. We discuss the implications of these restitution mechanisms for citrus breeding and lemon genetics.
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Affiliation(s)
- Houssem Rouiss
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de RoujolPetit-Bourg, Guadeloupe, France
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
| | - Patrick Ollitrault
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de RoujolPetit-Bourg, Guadeloupe, France
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
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25
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Cirmi S, Maugeri A, Ferlazzo N, Gangemi S, Calapai G, Schumacher U, Navarra M. Anticancer Potential of Citrus Juices and Their Extracts: A Systematic Review of Both Preclinical and Clinical Studies. Front Pharmacol 2017; 8:420. [PMID: 28713272 PMCID: PMC5491624 DOI: 10.3389/fphar.2017.00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/14/2017] [Indexed: 01/16/2023] Open
Abstract
Background: During the last decades, a huge body of evidence has been accumulated suggesting that Citrus fruits and their juices might have a role in preventing many diseases including cancer. Objective: To summarize the numerous evidences on the potential of Citrus juices and their extracts as anticancer agents. Data sources: A systematic review of articles written in English using MEDLINE (1946-present), EMBASE (1974-present) and Web of Sciences (1970-present) was performed independently by two reviewers. Search terms included Citrus, Citrus aurantifolia, Citrus sinensis, Citrus paradisi, Citrus fruits, Citrus fruits extract, cancer, neoplasm, neoplasia, tumor, metastasis, carcinogenesis, proliferation. The last search was performed on March 16th, 2017. Study selection: Study selection and systematic review were carried out in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Prior to the beginning of the review, Authors defined a checklist for inclusion criteria, thus including articles which meet the following: (i) published on peer-reviewed scientific journals; (ii) Citrus juice used alone; (iii) extracts derived from Citrus juice; (iii) for preclinical studies, an exposure time to Citrus juices and their extracts more than 24 h. Reviews, meta-analyses, conference abstracts and book chapters were excluded. Data extraction: Three reviewers independently performed the extraction of articles. Data synthesis: 22 papers met our inclusion criteria and were eligible for inclusion in the final review. According to the kind of study, the selected ones were further divided in preclinical (n = 20) and observational (n = 2) studies. Conclusion: The studies discussed in this review strongly corroborate the role of Citrus juices and their derivatives as potential resource against cancer.
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Affiliation(s)
- Santa Cirmi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy.,Prof. Antonio Imbesi FoundationMessina, Italy
| | - Alessandro Maugeri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy.,Prof. Antonio Imbesi FoundationMessina, Italy
| | - Nadia Ferlazzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy
| | - Sebastiano Gangemi
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy and Institute of Applied Sciences and Intelligent Systems, National Research CouncilPozzuoli, Italy
| | - Gioacchino Calapai
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of MessinaMessina, Italy
| | - Udo Schumacher
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-EppendorfHamburg, Germany
| | - Michele Navarra
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy
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26
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Zai X, Yang Q, Liu K, Li R, Qian M, Zhao T, Li Y, Yin Y, Dong D, Fu L, Li S, Xu J, Chen W. A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M. BMC Genomics 2017; 18:402. [PMID: 28535754 PMCID: PMC5442703 DOI: 10.1186/s12864-017-3800-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/16/2017] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Brucella spp. are Gram-negative, facultative intracellular pathogens that cause brucellosis in both humans and animals. The B. abortus vaccine strain 104 M is the only vaccine available in China for the prevention of brucellosis in humans. Although the B. abortus 104 M genome has been fully sequenced, the current genome annotations are not yet complete. In addition, the main mechanisms underpinning its residual toxicity and vaccine-induced immune protection have yet to be elucidated. Mapping the proteome of B. abortus 104 M will help to improve genome annotation quality, thereby facilitating a greater understanding of its biology. RESULTS In this study, we utilized a proteogenomic approach that combined subcellular fractionation and peptide fractionation to perform a whole-proteome analysis and genome reannotation of B. abortus 104 M using high-resolution mass spectrometry. In total, 1,729 proteins (56.3% of 3,072) including 218 hypothetical proteins were identified using the culture conditions that were employed this study. The annotations of the B. abortus 104 M genome were also refined following identification and validation by reverse transcription-PCR. In addition, 14 pivotal virulence factors and 17 known protective antigens known to be involved in residual toxicity and immune protection were confirmed at the protein level following induction by the 104 M vaccine. Moreover, a further insight into the cell biology of multichromosomal bacteria was obtained following the elucidation of differences in protein expression levels between the small and large chromosomes. CONCLUSIONS The work presented in this report used a proteogenomic approach to perform whole-proteome analysis and genome reannotation in B. abortus 104 M; this work helped to improve genome annotation quality. Our analysis of virulence factors, protective antigens and other protein effectors provided the basis for further research to elucidate the mechanisms of residual toxicity and immune protection induced by the 104 M vaccine. Finally, the potential link between replication dynamics, gene function, and protein expression levels in this multichromosomal bacterium was detailed.
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Affiliation(s)
- Xiaodong Zai
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Qiaoling Yang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Kun Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ruihua Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Mengying Qian
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Taoran Zhao
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yaohui Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ying Yin
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Dayong Dong
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ling Fu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Shanhu Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China.
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China.
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27
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Curtolo M, Cristofani-Yaly M, Gazaffi R, Takita MA, Figueira A, Machado MA. QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genomics 2017; 18:289. [PMID: 28403819 PMCID: PMC5389163 DOI: 10.1186/s12864-017-3629-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/14/2017] [Indexed: 11/24/2022] Open
Abstract
Background Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits. A controlled Murcott x Pera crossing was conducted at the Citrus Germplasm Repository at the Sylvio Moreira Citrus Centre of the Agronomic Institute (IAC) located in Cordeirópolis, SP, in 1997. In 2012, 278 F1 individuals out of a family of 312 confirmed hybrid individuals were analyzed for fruit traits and genotyped using the DArTseq markers. Using OneMap software to obtain the integrated genetic map, we considered only the DArT loci that showed no segregation deviation. The likelihood ratio and the genomic information from the available Citrus sinensis L. Osbeck genome were used to determine the linkage groups (LGs). Results The resulting integrated map contained 661 markers in 13 LGs, with a genomic coverage of 2,774 cM and a mean density of 0.23 markers/cM. The groups were assigned to the nine Citrus haploid chromosomes; however, some of the chromosomes were represented by two LGs due the lack of information for a single integration, as in cases where markers segregated in a 3:1 fashion. A total of 19 QTLs were identified through composite interval mapping (CIM) of the 12 analyzed fruit characteristics: fruit diameter (cm), height (cm), height/diameter ratio, weight (g), rind thickness (cm), segments per fruit, total soluble solids (TSS, %), total titratable acidity (TTA, %), juice content (%), number of seeds, TSS/TTA ratio and number of fruits per box. The genomic sequence (pseudochromosomes) of C. sinensis was compared to the genetic map, and synteny was clearly identified. Further analysis of the map regions with the highest LOD scores enabled the identification of putative genes that could be associated with the fruit quality characteristics. Conclusion An integrated linkage map of Murcott tangor and Pera sweet orange using DArTseq™ molecular markers was established and it was useful to perform QTL mapping of twelve fruit quality traits. The next generation sequences data allowed the comparison between the linkage map and the genomic sequence (pseudochromosomes) of C. sinensis and the identification of genes that may be responsible for phenotypic traits in Citrus. The obtained linkage map was used to assign sequences that had not been previously assigned to a position in the reference genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3629-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maiara Curtolo
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil.,Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Mariângela Cristofani-Yaly
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil.
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos (UFSCar) - Centro de Ciências Agrárias, Rodovia Anhanguera, km 174, 13600-970, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - Marcos Antonio Machado
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
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28
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Shimizu T, Kitajima A, Nonaka K, Yoshioka T, Ohta S, Goto S, Toyoda A, Fujiyama A, Mochizuki T, Nagasaki H, Kaminuma E, Nakamura Y. Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes. PLoS One 2016; 11:e0166969. [PMID: 27902727 PMCID: PMC5130255 DOI: 10.1371/journal.pone.0166969] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/07/2016] [Indexed: 01/07/2023] Open
Abstract
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy-Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.
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Affiliation(s)
- Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
- * E-mail:
| | - Akira Kitajima
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, Japan
| | - Keisuke Nonaka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Terutaka Yoshioka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Satoshi Ohta
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Shingo Goto
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takako Mochizuki
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Eli Kaminuma
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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29
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Oueslati A, Ollitrault F, Baraket G, Salhi-Hannachi A, Navarro L, Ollitrault P. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR. BMC Genet 2016; 17:118. [PMID: 27539067 PMCID: PMC4991024 DOI: 10.1186/s12863-016-0426-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/11/2016] [Indexed: 11/28/2022] Open
Abstract
Background Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. Results The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the “true citrus” genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. Conclusions We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at subfamily level. The robustness of this genotyping method is an additional decisive advantage for network collaborative research. The availability of WGS data for the main “true citrus” species should soon make it possible to develop a set of DSNP markers allowing very fine resolution of this very important horticultural group. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0426-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amel Oueslati
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie LR99ES12, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Campus Universitaire, El Manar-Tunis, 2092, Tunisia.,UMR Agap, CIRAD, Petit-Bourg, F-97170, Guadeloupe, France
| | - Frederique Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain
| | - Ghada Baraket
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie LR99ES12, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Campus Universitaire, El Manar-Tunis, 2092, Tunisia
| | - Amel Salhi-Hannachi
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie LR99ES12, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Campus Universitaire, El Manar-Tunis, 2092, Tunisia
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain
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Cytoplasmic diversity, phylogenetic relationships and molecular evolution of Tunisian Citrus species as inferred from mutational events and pseudogene of chloroplast trnL-trnF spacer. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Aleza P, Cuenca J, Juárez J, Navarro L, Ollitrault P. Inheritance in doubled-diploid clementine and comparative study with SDR unreduced gametes of diploid clementine. PLANT CELL REPORTS 2016; 35:1573-86. [PMID: 27038940 DOI: 10.1007/s00299-016-1972-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/21/2016] [Indexed: 05/23/2023]
Abstract
Tetraploid clementine displays mainly tetrasomic inheritance. Genetic structures of 2n SDR and 2 × gametes from DD clementine are complementary and will guides triploids citrus breeding strategies. Triploid breeding is developed worldwide to create new seedless cultivars. Citrus triploid hybrids can be recovered from 2x × 2x sexual hybridizations as a consequence of the formation of unreduced gametes (2n), or from 4x × 2x interploid hybridizations in which tetraploid parents used are most often doubled-diploid (DD). Here we have analyzed the inheritance in doubled-diploid clementine and compared the genetic structures of gametes of DD clementine with SDR unreduced gametes of diploid clementine. Parental heterozygosity restitution (PHR) with DD parents depends on the rate of preferential chromosome pairing and thus the proportion of disomic versus tetrasomic segregations. Doubled-diploid clementine largely exhibited tetrasomic segregation. However, three linkage groups had intermediate segregation and one had a tendency for disomy. Significant doubled reduction rates (DR) rates were observed in six of the nine LGs. Differences of PHR between 2n SDR and 2x DD gametes were highest in the centromeric region and progressively decreased toward the distal regions where they were not significant. Over all markers, PHR was lower (two-thirds) in SDR 2n gametes than in DD-derived diploid gametes. The two strategies appear complementary in terms of genotypic variability. Interploid 4x × 2x hybridization is potentially more efficient for developing new cultivars that are phenotypically closer to the diploid parent of the DD than sexual hybridization through SDR 2n gametes. Conversely, 2x × 2x triploidisation has the potential to produce novel products with characteristics for market segmentation strategies.
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Affiliation(s)
- P Aleza
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - J Cuenca
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - J Juárez
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - L Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain.
| | - P Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain.
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de Roujol, 97170, Petit-Bourg, Guadeloupe.
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Vishnu US, Sankarasubramanian J, Gunasekaran P, Sridhar J, Rajendhran J. Omics of Brucella: Species-Specific sRNA-Mediated Gene Ontology Regulatory Networks Identified by Computational Biology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:375-85. [DOI: 10.1089/omi.2016.0034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Udayakumar S. Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Paramasamy Gunasekaran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Jayavel Sridhar
- Department of Biotechnology, DDE, Madurai Kamaraj University, Madurai, India
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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Tarasov VA, Makhotkin MA, Shin EF, Boiko NV, Tyutyakina MG, Chikunov IE, Naboka AV, Mashkarina AN, Kirpii AA, Matishov DG. Change in the selection of microRNA strands during DNA damage induction. DOKL BIOCHEM BIOPHYS 2016; 467:99-101. [PMID: 27193708 DOI: 10.1134/s160767291602006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 11/22/2022]
Abstract
It was first shown that DNA damage induction in mitomycin C-treated HeLa cells leads to a change in the selection of 5p and 3p microRNA duplex strands in the formation of the RNA-induced silencing complex (RISC).
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Affiliation(s)
- V A Tarasov
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | - M A Makhotkin
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia.
| | - E F Shin
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | - N V Boiko
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | - M G Tyutyakina
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | - I E Chikunov
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | - A V Naboka
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | - A N Mashkarina
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
| | | | - D G Matishov
- Institute of Arid Zones, Southern Scientific Center, Russian Academy of Sciences, pr. Chekhova 41, Rostov-on-Don, 3444006, Russia
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Curk F, Ollitrault F, Garcia-Lor A, Luro F, Navarro L, Ollitrault P. Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. ANNALS OF BOTANY 2016; 117:565-83. [PMID: 26944784 PMCID: PMC4817432 DOI: 10.1093/aob/mcw005] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/21/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The origin of limes and lemons has been a source of conflicting taxonomic opinions. Biochemical studies, numerical taxonomy and recent molecular studies suggested that cultivated Citrus species result from interspecific hybridization between four basic taxa (C. reticulata,C. maxima,C. medica and C. micrantha). However, the origin of most lemons and limes remains controversial or unknown. The aim of this study was to perform extended analyses of the diversity, genetic structure and origin of limes and lemons. METHODS The study was based on 133 Citrus accessions. It combined maternal phylogeny studies based on mitochondrial and chloroplastic markers, and nuclear structure analysis based on the evaluation of ploidy level and the use of 123 markers, including 73 basic taxa diagnostic single nucleotide polymorphism (SNP) and indel markers. KEY RESULTS The lime and lemon horticultural group appears to be highly polymorphic, with diploid, triploid and tetraploid varieties, and to result from many independent reticulation events which defined the sub-groups. Maternal phylogeny involves four cytoplasmic types out of the six encountered in the Citrus genus. All lime and lemon accessions were highly heterozygous, with interspecific admixture of two, three and even the four ancestral taxa genomes. Molecular polymorphism between varieties of the same sub-group was very low. CONCLUSIONS Citrus medica contributed to all limes and lemons and was the direct male parent for the main sub-groups in combination with C. micrantha or close papeda species (for C. aurata, C. excelsa, C. macrophylla and C. aurantifolia--'Mexican' lime types of Tanaka's taxa), C. reticulata(for C. limonia, C. karna and C. jambhiri varieties of Tanaka's taxa, including popular citrus rootstocks such as 'Rangpur' lime, 'Volkamer' and 'Rough' lemons), C. aurantium (for C. limetta and C. limon--yellow lemon types--varieties of Tanaka's taxa) or the C. maxima × C. reticulate hybrid (for C. limettioides--'Palestine sweet' lime types--and C. meyeri). Among triploid limes, C. latifolia accessions ('Tahiti' and 'Persian' lime types) result from the fertilization of a haploid ovule of C. limon by a diploid gamete of C. aurantifolia, while C. aurantifolia triploid accessions ('Tanepao' lime types and 'Madagascar' lemon) probably result from an interspecific backcross (a diploid ovule of C. aurantifolia fertilized by C. medica). As limes and lemons were vegetatively propagated (apomixis, horticultural practices) the intra-sub-group phenotypic diversity results from asexual variations.
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Affiliation(s)
- Franck Curk
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Frédérique Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Andres Garcia-Lor
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - François Luro
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Station de Roujol, F-97170, Petit-Bourg, Guadeloupe, France
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Dugrand-Judek A, Olry A, Hehn A, Costantino G, Ollitrault P, Froelicher Y, Bourgaud F. The Distribution of Coumarins and Furanocoumarins in Citrus Species Closely Matches Citrus Phylogeny and Reflects the Organization of Biosynthetic Pathways. PLoS One 2015; 10:e0142757. [PMID: 26558757 PMCID: PMC4641707 DOI: 10.1371/journal.pone.0142757] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Citrus plants are able to produce defense compounds such as coumarins and furanocoumarins to cope with herbivorous insects and pathogens. In humans, these chemical compounds are strong photosensitizers and can interact with medications, leading to the "grapefruit juice effect". Removing coumarins and furanocoumarins from food and cosmetics imply additional costs and might alter product quality. Thus, the selection of Citrus cultivars displaying low coumarin and furanocoumarin contents constitutes a valuable alternative. In this study, we performed ultra-performance liquid chromatography coupled with mass spectrometry analyses to determine the contents of these compounds within the peel and the pulp of 61 Citrus species representative of the genetic diversity all Citrus. Generally, Citrus peel contains larger diversity and higher concentrations of coumarin/furanocoumarin than the pulp of the same fruits. According to the chemotypes found in the peel, Citrus species can be separated into 4 groups that correspond to the 4 ancestral taxa (pummelos, mandarins, citrons and papedas) and extended with their respective secondary species descendants. Three of the 4 ancestral taxa (pummelos, citrons and papedas) synthesize high amounts of these compounds, whereas mandarins appear practically devoid of them. Additionally, all ancestral taxa and their hybrids are logically organized according to the coumarin and furanocoumarin pathways described in the literature. This organization allows hypotheses to be drawn regarding the biosynthetic origin of compounds for which the biogenesis remains unresolved. Determining coumarin and furanocoumarin contents is also helpful for hypothesizing the origin of Citrus species for which the phylogeny is presently not firmly established. Finally, this work also notes favorable hybridization schemes that will lead to low coumarin and furanocoumarin contents, and we propose to select mandarins and Ichang papeda as Citrus varieties for use in creating species devoid of these toxic compounds in future breeding programs.
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Affiliation(s)
- Audray Dugrand-Judek
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alexandre Olry
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alain Hehn
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | | | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113 Moncada, Valencia, Spain
- CIRAD, UMR AGAP, Station de Roujol, 97170 Petit-Bourg, Guadeloupe, France
| | - Yann Froelicher
- CIRAD, UMR AGAP, Station INRA, F-20230, San Giuliano, France
| | - Frédéric Bourgaud
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
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Thi Nguyen TT, Thi Tran TT, Hua TM, Diep TT, Chau DKN, Duus F, Le TN. Investigation of peel and leaf essential oils ofCitrus clementinaHort. ex Tan. growing in the south of Vietnam. JOURNAL OF ESSENTIAL OIL RESEARCH 2015. [DOI: 10.1080/10412905.2015.1083491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Leduc A, Traoré YN, Boyer K, Magne M, Grygiel P, Juhasz CC, Boyer C, Guerin F, Wonni I, Ouedraogo L, Vernière C, Ravigné V, Pruvost O. Bridgehead invasion of a monomorphic plant pathogenic bacterium:Xanthomonas citripv. citri, an emerging citrus pathogen in Mali and Burkina Faso. Environ Microbiol 2015; 17:4429-42. [DOI: 10.1111/1462-2920.12876] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
Affiliation(s)
- A. Leduc
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | | | - K. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - M. Magne
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - P. Grygiel
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. C. Juhasz
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - F. Guerin
- UMR PVBMT; Université de la Réunion; 97410 Saint Pierre La Réunion France
| | - I. Wonni
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - L. Ouedraogo
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - C. Vernière
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - V. Ravigné
- UMR BGPI; CIRAD; 34398 Montpellier France
| | - O. Pruvost
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
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Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties. PLoS One 2015; 10:e0125628. [PMID: 25973611 PMCID: PMC4431842 DOI: 10.1371/journal.pone.0125628] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/16/2015] [Indexed: 11/19/2022] Open
Abstract
Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.
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Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J. A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Mol Biol Evol 2015; 32:2015-35. [PMID: 25873589 PMCID: PMC4833069 DOI: 10.1093/molbev/msv082] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here, we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels (insertions and deletions), and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analyzed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection.
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Affiliation(s)
- Jose Carbonell-Caballero
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Roberto Alonso
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Victoria Ibañez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain
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Hulse-Kemp AM, Ashrafi H, Stoffel K, Zheng X, Saski CA, Scheffler BE, Fang DD, Chen ZJ, Van Deynze A, Stelly DM. BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping. G3 (BETHESDA, MD.) 2015; 5:1095-105. [PMID: 25858960 PMCID: PMC4478540 DOI: 10.1534/g3.115.017749] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/30/2015] [Indexed: 11/25/2022]
Abstract
A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas 77843
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Kevin Stoffel
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Xiuting Zheng
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Christopher A Saski
- Clemson University Genomics Institute, Clemson University, Clemson, South Carolina 29634
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi 38766
| | - David D Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas 77843
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Liang M, Yang X, Li H, Su S, Yi H, Chai L, Deng X. De novo transcriptome assembly of pummelo and molecular marker development. PLoS One 2015; 10:e0120615. [PMID: 25799271 PMCID: PMC4370633 DOI: 10.1371/journal.pone.0120615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/24/2015] [Indexed: 11/19/2022] Open
Abstract
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.
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Affiliation(s)
- Mei Liang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaoming Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hang Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shiying Su
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hualin Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Aleza P, Cuenca J, Hernández M, Juárez J, Navarro L, Ollitrault P. Genetic mapping of centromeres in the nine Citrus clementina chromosomes using half-tetrad analysis and recombination patterns in unreduced and haploid gametes. BMC PLANT BIOLOGY 2015; 15:80. [PMID: 25848689 PMCID: PMC4367916 DOI: 10.1186/s12870-015-0464-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/20/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Mapping centromere locations in plant species provides essential information for the analysis of genetic structures and population dynamics. The centromere's position affects the distribution of crossovers along a chromosome and the parental heterozygosity restitution by 2n gametes is a direct function of the genetic distance to the centromere. Sexual polyploidisation is relatively frequent in Citrus species and is widely used to develop new seedless triploid cultivars. The study's objectives were to (i) map the positions of the centromeres of the nine Citrus clementina chromosomes; (ii) analyse the crossover interference in unreduced gametes; and (iii) establish the pattern of genetic recombination in haploid clementine gametes along each chromosome and its relationship with the centromere location and distribution of genic sequences. RESULTS Triploid progenies were derived from unreduced megagametophytes produced by second-division restitution. Centromere positions were mapped genetically for all linkage groups using half-tetrad analysis. Inference of the physical locations of centromeres revealed one acrocentric, four metacentric and four submetacentric chromosomes. Crossover interference was observed in unreduced gametes, with variation seen between chromosome arms. For haploid gametes, a strong decrease in the recombination rate occurred in centromeric and pericentromeric regions, which contained a low density of genic sequences. In chromosomes VIII and IX, these low recombination rates extended beyond the pericentromeric regions. The genomic region corresponding to a genetic distance < 5cM from a centromere represented 47% of the genome and 23% of the genic sequences. CONCLUSIONS The centromere positions of the nine citrus chromosomes were genetically mapped. Their physical locations, inferred from the genetic ones, were consistent with the sequence constitution and recombination pattern along each chromosome. However, regions with low recombination rates extended beyond the pericentromeric regions of some chromosomes into areas richer in genic sequences. The persistence of strong linkage disequilibrium between large numbers of genes promotes the stability of epistatic interactions and multilocus-controlled traits over successive generations but also maintains multi-trait associations. Identification of the centromere positions will allow the development of simple methods to analyse unreduced gamete formation mechanisms in a large range of genotypes and further modelling of genetic inheritance in sexual polyploidisation breeding schemes.
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Affiliation(s)
- Pablo Aleza
- />Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia Spain
| | - José Cuenca
- />Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia Spain
| | - María Hernández
- />Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia Spain
| | - José Juárez
- />Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia Spain
| | - Luis Navarro
- />Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia Spain
| | - Patrick Ollitrault
- />Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia Spain
- />CIRAD, UMR AGAP, Avenue Agropolis - TA A-75/02 F‐34398, Montpellier, France
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Curk F, Ancillo G, Garcia-Lor A, Luro F, Perrier X, Jacquemoud-Collet JP, Navarro L, Ollitrault P. Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2. BMC Genet 2014; 15:152. [PMID: 25544367 PMCID: PMC4302129 DOI: 10.1186/s12863-014-0152-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2. RESULTS 454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2. CONCLUSIONS 454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes.
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Affiliation(s)
- Franck Curk
- UMR AGAP, Institut National de la Recherche Agronomique (Inra), Centre Inra de Corse, F-20230, San Giuliano, France.
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Gema Ancillo
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Andres Garcia-Lor
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - François Luro
- UMR AGAP, Institut National de la Recherche Agronomique (Inra), Centre Inra de Corse, F-20230, San Giuliano, France.
| | - Xavier Perrier
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398, Montpellier, Cedex 5, France.
| | - Jean-Pierre Jacquemoud-Collet
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398, Montpellier, Cedex 5, France.
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398, Montpellier, Cedex 5, France.
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Dang Y, Wang YC, Huang QJ. Microarray and Next-Generation Sequencing to Analyse Gastric Cancer. Asian Pac J Cancer Prev 2014. [DOI: 10.7314/apjcp.2014.15.19.8035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Zhong X, Li Q, Yu H, Kong L. SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. PLoS One 2014; 9:e108256. [PMID: 25238392 PMCID: PMC4169597 DOI: 10.1371/journal.pone.0108256] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/28/2014] [Indexed: 01/07/2023] Open
Abstract
Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crassostrea. In the study, 57 novel SNPs were developed from an EST database of C. gigas by the HRM (high-resolution melting) method. Transferability of 377 SNPs developed for C. gigas was examined on four other Crassostrea species: C. sikamea, C. angulata, C. hongkongensis and C. ariakensis. Among the 377 primer pairs tested, 311 (82.5%) primers showed amplification in C. sikamea, 353 (93.6%) in C. angulata, 254 (67.4%) in C. hongkongensis and 253 (67.1%) in C. ariakensis. A total of 214 SNPs were found to be transferable to all four species. Phylogenetic analyses showed that C. hongkongensis was a sister species of C. ariakensis and that this clade was sister to the clade containing C. sikamea, C. angulata and C. gigas. Within this clade, C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister group. In addition, we detected eight SNPs as potentially being under selection by two outlier tests (fdist and hierarchical methods). The SNPs studied here should be useful for genetic diversity, comparative mapping and phylogenetic studies across species in Crassostrea and the candidate outlier SNPs are worth exploring in more detail regarding association genetics and functional studies.
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Affiliation(s)
- Xiaoxiao Zhong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
- * E-mail:
| | - Hong Yu
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
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Liu S, Khan MRG, Li Y, Zhang J, Hu C. Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization. Mol Genet Genomics 2014; 289:855-72. [PMID: 24820208 DOI: 10.1007/s00438-014-0858-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/19/2014] [Indexed: 11/26/2022]
Abstract
The CCCH-type zinc finger proteins comprise a large gene family of regulatory proteins and are widely distributed in eukaryotic organisms. The CCCH proteins have been implicated in multiple biological processes and environmental responses in plants. Little information is available, however, about CCCH genes in plants, especially in woody plants such as citrus. The release of the whole-genome sequence of citrus allowed us to perform a genome-wide analysis of CCCH genes and to compare the identified proteins with their orthologs in model plants. In this study, 62 CCCH genes and a total of 132 CCCH motifs were identified, and a comprehensive analysis including the chromosomal locations, phylogenetic relationships, functional annotations, gene structures and conserved motifs was performed. Distribution mapping revealed that 54 of the 62 CCCH genes are unevenly dispersed on the nine citrus chromosomes. Based on phylogenetic analysis and gene structural features, we constructed 5 subfamilies of 62 CCCH members and integrative subfamilies from citrus, Arabidopsis, and rice, respectively. Importantly, large numbers of SNPs and InDels in 26 CCCH genes were identified from Poncirus trifoliata and Fortunella japonica using whole-genome deep re-sequencing. Furthermore, citrus CCCH genes showed distinct temporal and spatial expression patterns in different developmental processes and in response to various stress conditions. Our comprehensive analysis of CleC3Hs is a valuable resource that further elucidates the roles of CCCH family members in plant growth and development. In addition, variants and comparative genomics analyses deepen our understanding of the evolution of the CCCH gene family and will contribute to further genetics and genomics studies of citrus and other plant species.
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Affiliation(s)
- Shengrui Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
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Wu B, Zhong GY, Yue JQ, Yang RT, Li C, Li YJ, Zhong Y, Wang X, Jiang B, Zeng JW, Zhang L, Yan ST, Bei XJ, Zhou DG. Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments. PLoS One 2014; 9:e94506. [PMID: 24732455 PMCID: PMC3986212 DOI: 10.1371/journal.pone.0094506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/17/2014] [Indexed: 11/18/2022] Open
Abstract
Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.
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Affiliation(s)
- Bo Wu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guang-yan Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
| | - Jian-qiang Yue
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China
| | - Run-ting Yang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chong Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yue-jia Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yun Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuan Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Bo Jiang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ji-wu Zeng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Li Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shu-tang Yan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xue-jun Bei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Dong-guo Zhou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China
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Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS One 2013; 8:e78680. [PMID: 24236035 PMCID: PMC3827278 DOI: 10.1371/journal.pone.0078680] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/15/2013] [Indexed: 01/01/2023] Open
Abstract
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction.
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Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 2013; 8:e77022. [PMID: 24155917 PMCID: PMC3796552 DOI: 10.1371/journal.pone.0077022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022] Open
Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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Affiliation(s)
- Sara Montanari
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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Cuenca J, Aleza P, Vicent A, Brunel D, Ollitrault P, Navarro L. Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes. PLoS One 2013; 8:e76755. [PMID: 24116149 PMCID: PMC3792864 DOI: 10.1371/journal.pone.0076755] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/23/2013] [Indexed: 12/17/2022] Open
Abstract
Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.
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Affiliation(s)
- José Cuenca
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias. Moncada, Valencia, Spain
| | - Pablo Aleza
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias. Moncada, Valencia, Spain
| | - Antonio Vicent
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias. Moncada, Valencia, Spain
| | - Dominique Brunel
- Etude du Polymorphisme des Genomes Vegetaux, Institut National de la Recherche Agronomique, Évry, France
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias. Moncada, Valencia, Spain
- Etude du Polymorphisme des Genomes Vegetaux, Institut National de la Recherche Agronomique, Évry, France
- BIOS Department, Amélioration Génétique des Espèces à Multiplication Végétative. Centre de Coopeération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias. Moncada, Valencia, Spain
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