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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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Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep 2023; 13:10919. [PMID: 37407627 DOI: 10.1038/s41598-023-37024-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
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Affiliation(s)
- Jagveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- Department of Fruit Science, College of Horticulture & Forestry, Acharya Narendra Deva University of Agricultural & Technology, Kumarganj, 224229, India
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Vishal Sharma
- National Agri-Food Biotechnology Institute, Sector-81, SAS Nagar, Mohali, Punjab, 140308, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173229, India
| | - Popat Nanaso Gaikwad
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurupkar Singh Sidhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Nimarpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Taveena Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - H S Rattanpal
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, 141004, India
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Reuse of Food Waste: The Chemical Composition and Health Properties of Pomelo ( Citrus maxima) Cultivar Essential Oils. Molecules 2022; 27:molecules27103273. [PMID: 35630750 PMCID: PMC9146573 DOI: 10.3390/molecules27103273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
The aim of the present study is to investigate the chemical profile, antioxidant activity, carbohydrate-hydrolysing enzyme inhibition, and hypolipidemic effect of essential oils (EOs) extracted from Sicilian Citrus maxima (pomelo) flavedo. Using gas-chromatography-mass spectrometry analysis (GC-MS) we analysed the Eos of five cultivars of C. maxima, namely, ‘Chadock’, ‘Maxima’, ‘Pyriformis’, ‘Terracciani’, and ‘Todarii’, and their blends. The antioxidant activity was performed by using a multi-target approach using 2,2′-Azino-Bis-3-Ethylbenzothiazoline-6-Sulfonic acid (ABTS), 2,2-Diphenyl-1-picrylhydrazyl (DPPH), ferric reducing ability power (FRAP), and β-carotene bleaching tests. The α-amylase, α-glucosidase, and lipase-inhibitory activities were also assessed. GC-MS analyses revealed D-limonene as the main monoterpene hydrocarbon in all cultivars, albeit with different percentages in the range of 21.72–71.13%. A good content of oxygenated monoterpenes was detected for all cultivars, especially for ‘Todarii’. The analysis of the principal components (PCA), and related clusters (HCA), was performed to find chemo-diversity among the analysed samples. EOs from ‘Chadock’ and ‘Maxima’ were statistically similar to each other, and they differed from P3 in the smaller amount of sesquiterpene hydrocarbons, while the oils from ‘Terracciani’ and ‘Todarii’ were found to be chemically and statistically different. ‘Chadock’ EO was the most active to scavenge radicals (IC50 values of 22.24 and 27.23 µg/mL in ABTS and DPPH tests, respectively). ‘Terracciani’ EO was the most active against both lipase and α-amylase, whereas the blends obtained by the combination (1:1 v/v) of C. maxima ‘Maxima’ + ‘Todarii’ were the most active against α-glucosidase. Generally, the blends did not exert a unique behaviour in potentiating or reducing the bioactivity of the pomelo EOs.
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Physiological and Biochemical Adaptive Traits in Leaves of Four Citrus Species Grown in an Italian Charterhouse. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Citrus trees are a very important crops that are cultivated worldwide, but not much knowledge is known about the ecophysiological responses to climatic changes in trees under natural conditions. The aim of this study was to investigate their adaptive capacity in response to seasonal phenological and environmental changes. The trial included Citrus trees (sweet orange, bitter orange, lemon, mandarin) growing under non-regular cropping conditions in a Monumental Charterhouse in Tuscany, in a subtropical Mediterranean climate with hot summer conditions. During a 1-year field trial, we determined the variations in chlorophyll fluorescence parameters and leaf biochemical traits (content of chlorophylls and carotenoids, total phenolic content (TPC), total antioxidant capacity (TAC), and total non-structural carbohydrates). In all Citrus spp., interspecific mean values of photochemical efficiency peaked during the summer, while a marked photoinhibition occurred in the winter in concomitance with higher interspecific mean values of leaf TPC, TAC, and non-structural carbohydrates. The trees showed the pivotal role played by photosynthetic acclimation as a survival strategy to tolerate abiotic stress in the climate change hotspot of Mediterranean environment. This study is included in a wider project aimed at a new valorization of Citrus trees as genetic resource and its by-products with added-value applications for innovative functional foods.
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Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
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Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
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Demarcq B, Cavailles M, Lambert L, Schippa C, Ollitrault P, Luro F. Characterization of Odor-Active Compounds of Ichang Lemon ( Citrus wilsonii Tan.) and Identification of Its Genetic Interspecific Origin by DNA Genotyping. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3175-3188. [PMID: 33667086 DOI: 10.1021/acs.jafc.0c07894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ichang lemon is a citrus fruit whose rind gives off a delicious and much appreciated fragrance and flavor. The volatile components of the fruit peel of Ichang lemon were investigated by GC-MS and GC-O (AEDA method). Simultaneously, its genetic origin was identified by using diagnostic SNP markers specific to ancestral species and multiallelic SSR and InDel markers. Ichang lemon combines three ancestral genomes (Citrus maxima, Citrus ichangensis, and Citrus reticulata) and may be a pummelo × Yuzu hybrid. Although the major compounds of the Ichang lemon aromatic profile were present in Citrus junos, a few pummelo-specific compounds were also detected, such as indole and nootkatone, in agreement with its maternal lineage. 3-Methyl-3-sulfanylbutyl acetate, reported to occur in passion fruit and brewed coffee, was identified by GC-MS, GC-QTOF-MS, and GC-FTIR for the first time in citrus. This odor-active compound has a sulfurous, tropical fruity, green note.
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Affiliation(s)
- Benoit Demarcq
- V Mane Fils SA, 620 Route de Grasse, 06620 Le Bar-sur-Loup, France
| | | | - Laetitia Lambert
- V Mane Fils SA, 620 Route de Grasse, 06620 Le Bar-sur-Loup, France
| | | | - Patrick Ollitrault
- CIRAD, UMR AGAP, F-20230 San Giuliano, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France
| | - Francois Luro
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France
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Ahmed D, Curk F, Evrard JC, Froelicher Y, Ollitrault P. Preferential Disomic Segregation and C. micrantha/C. medica Interspecific Recombination in Tetraploid 'Giant Key' Lime; Outlook for Triploid Lime Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:939. [PMID: 32670332 PMCID: PMC7330052 DOI: 10.3389/fpls.2020.00939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 06/09/2020] [Indexed: 05/14/2023]
Abstract
The triploid 'Tahiti' lime (C. x latifolia (Yu. Tanaka) Tanaka) naturally originated from a merger between a haploid ovule of lemon (C. x limon (L.) Burm) and a diploid pollen from a 'Mexican' lime (C. x aurantiifolia (Christm.) Swing). The very limited natural inter-varietal diversity and gametic sterility of C. latifolia requires a phylogenomic based reconstruction breeding strategy to insure its diversification. We developed a strategy based on interploid hybridization between diploid lemon and the doubled diploid 'Giant Key' lime. This lime is a doubled diploid of 'Mexican' lime, itself a natural interspecific F1 hybrid between C. medica L. and C. micrantha Wester. For an optimized breeding program, we analyzed the meiotic behavior of the allotetraploid lime, the genetic structure of its diploid gametes, the interspecific recombination between C. medica and C. micrantha, and constructed its genetic map. A population of 272 triploid hybrids was generated using 'Giant Key' lime as pollinator. One hundred fifty-eight SNPs diagnostic of C. micrantha, regularly distributed throughout the citrus genome were successfully developed and applied. The genetic structure of the diploid gametes was examined based on C. micrantha doses along the genome. The diploid gametes transmitted in average 91.17% of the parental interspecific C. medica/C. micrantha heterozygosity. Three chromosomes (2, 8, and 9) showed disomic segregation with high preferential pairing values, while the remaining chromosomes showed an intermediate inheritance with a preferential disomic trend. A total of 131 SNPs were assigned to nine linkage groups to construct the genetic map. It spanned 272.8 cM with a low average recombination rate (0.99 cM Mb-1) and high synteny and colinearity with the reference clementine genome. Our results confirmed that an efficient reconstruction breeding strategy for 'Tahiti' lime is possible, based on interploid hybridization using a doubled diploid of C. aurantiifolia. The tetraploid parent should be selected for favorable agronomic traits and its genetic value should be efficiently inherited by the progeny thanks to transmission of the high level of parental heterozygosity. However, it would require developing numerous progeny to overcome the linkage drag caused by the limited interspecific recombination associated with the predominant disomic inheritance.
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Affiliation(s)
- Dalel Ahmed
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, San Giuliano, France
| | - Franck Curk
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Ly SN, Garavito A, De Block P, Asselman P, Guyeux C, Charr JC, Janssens S, Mouly A, Hamon P, Guyot R. Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae. PLoS One 2020; 15:e0232295. [PMID: 32353023 PMCID: PMC7192488 DOI: 10.1371/journal.pone.0232295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/11/2020] [Indexed: 11/19/2022] Open
Abstract
In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.
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Affiliation(s)
- Serigne Ndiawar Ly
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Andrea Garavito
- Departamento Ciencias Biológicas, Universidad de Caldas, Manizales, Colombia
| | | | - Pieter Asselman
- Meise Botanic Garden, Meise, Belgium
- University of Ghent, Ghent, Belgium
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Arnaud Mouly
- Laboratory Chrono-Environment, UMR CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
- Besançon Botanic Garden, Université de Bourgogne Franche-Comté, Besançon, France
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia
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Gemenet DC, Kitavi MN, David M, Ndege D, Ssali RT, Swanckaert J, Makunde G, Yencho GC, Gruneberg W, Carey E, Mwanga RO, Andrade MI, Heck S, Campos H. Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs. PLoS One 2020; 15:e0232173. [PMID: 32330201 PMCID: PMC7182229 DOI: 10.1371/journal.pone.0232173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/08/2020] [Indexed: 11/19/2022] Open
Abstract
Quality assurance and control (QA/QC) is an essential element of a breeding program's optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)'s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers' fields. The study also enabled evaluation of CIP's global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.
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Affiliation(s)
| | - Mercy N. Kitavi
- International Potato Center (CIP), ILRI Campus, Nairobi, Kenya
| | - Maria David
- International Potato Center (CIP), Apartado, Lima, Peru
| | - Dorcah Ndege
- International Potato Center (CIP), ILRI Campus, Nairobi, Kenya
| | | | | | | | - G. Craig Yencho
- North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Edward Carey
- International Potato Center (CIP), Kumasi, Ghana
| | | | | | - Simon Heck
- International Potato Center (CIP), ILRI Campus, Nairobi, Kenya
| | - Hugo Campos
- International Potato Center (CIP), Apartado, Lima, Peru
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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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Cottin A, Penaud B, Glaszmann JC, Yahiaoui N, Gautier M. Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes. G3 (BETHESDA, MD.) 2020; 10:569-579. [PMID: 31862786 PMCID: PMC7003078 DOI: 10.1534/g3.119.400873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios that can be encountered in plant species. For this, we developed an R package to simulate genotyping data under such scenarios. The tested inference methods performed similarly well as far as representatives of source populations were available. As expected, the higher the level of differentiation between ancestral source populations and the lower the number of generations since admixture, the more accurate were the results. Interestingly, the accuracy of the methods was only marginally affected by i) the number of ancestries (up to six tested); ii) the sample design (i.e., unbalanced representation of source populations); and iii) the reproduction mode (e.g., selfing, vegetative propagation). If a source population was not represented in the data set, no bias was observed in inference accuracy for regions originating from represented sources and regions from the missing source were assigned differently depending on the methods. Overall, the selected ancestry inference methods may be used for crop plant analysis if all ancestral sources are known.
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Affiliation(s)
- Aurélien Cottin
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France, and
| | - Benjamin Penaud
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France, and
| | - Jean-Christophe Glaszmann
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France, and
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, F-34398 Montpellier, France,
- AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France, and
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12
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Hyun DY, Sebastin R, Lee KJ, Lee GA, Shin MJ, Kim SH, Lee JR, Cho GT. Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:688. [PMID: 32625218 PMCID: PMC7311657 DOI: 10.3389/fpls.2020.00688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/30/2020] [Indexed: 05/17/2023]
Abstract
Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.
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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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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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Gomes Ferreira MD, Araújo Castro J, Santana Silva RJ, Micheli F. HVA22 from citrus: A small gene family whose some members are involved in plant response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:395-404. [PMID: 31408843 DOI: 10.1016/j.plaphy.2019.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 05/27/2023]
Abstract
The HVA22 gene has been isolated for the first time from the aleurone layer of barley (Hordeum vulgare). Here, we characterized the HVA22 family from citrus (C. clementina and C. sinensis). Twelve genes, 6 in each species, were identified as well as duplication events for some of them. The ORF size ranged from 235 to 804 bp and the protein molecular weight from 94 to 267 kDa. All the citrus HVA22 protein presented transmembrane location and conserved TB2/DP1/HVA22 region. Phylogenetic and gene expression analyses suggested that some citrus HVA22 play a role in flower and fruit development, and that gene expression may be regulated by hormone or environmental conditions. Other regulation levels were also predicted, such as alternative splicing and post-translational modifications. The overall data indicated that citrus HVA22 may be involved in vesicular traffic in stressed cells, and that CcHVA22d could be involved in dehydration tolerance.
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Affiliation(s)
| | - Jacqueline Araújo Castro
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil; Instituto Federal de Educação, Ciência e Tecnologia Baiano (IFBaiano), Governador Mangabeira, Bahia, Brazil
| | - Raner José Santana Silva
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil; CIRAD, UMR AGAP, F-34398, Montpellier, France.
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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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De Ollas C, Morillón R, Fotopoulos V, Puértolas J, Ollitrault P, Gómez-Cadenas A, Arbona V. Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:427. [PMID: 31057569 PMCID: PMC6477659 DOI: 10.3389/fpls.2019.00427] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Raphaël Morillón
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, France
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Jaime Puértolas
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San-Giuliano, France
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
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18
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Viglietti G, Galla G, Porceddu A, Barcaccia G, Curk F, Luro F, Scarpa GM. Karyological Analysis and DNA Barcoding of Pompia Citron: A First Step toward the Identification of Its Relatives. PLANTS 2019; 8:plants8040083. [PMID: 30935148 PMCID: PMC6524030 DOI: 10.3390/plants8040083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/24/2019] [Accepted: 03/28/2019] [Indexed: 12/04/2022]
Abstract
Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the DNA content and to reconstruct the karyotype of several Pompia accessions. Molecular data from plastid DNA barcoding and nuclear DNA sequencing were used to study the genetic distance between Pompia and other citrus species. Flow cytometric estimates of DNA content and somatic chromosome counts suggest that Pompia is a regular diploid Citrus species. DNA polymorphisms of nuclear and chloroplast markers allowed us to investigate the genetic relationships between Pompia accessions and other Citrus species. Based on DNA polymorphism data we propose that Pompia is a very recent interspecific hybrid generated by a cross between C. aurantium (as seed bearer) and C. medica (as pollen donor). Our findings pave the way for further and more specific investigations of local Pompia germplasm resources that may help the preservation and valorisation of this valuable citrus fruit tree.
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Affiliation(s)
- Grazia Viglietti
- Dipartimento di AGRARIA Research Unit SACEG, University of Sassari, 07100 Sassari, Italy.
| | - Giulio Galla
- Laboratory of Genomics, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Padova, Italy.
| | - Andrea Porceddu
- Dipartimento di AGRARIA Research Unit SACEG, University of Sassari, 07100 Sassari, Italy.
| | - Gianni Barcaccia
- Laboratory of Genomics, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Padova, Italy.
| | - Frank Curk
- Unite Mixte de Recherche Amelioration Genetique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France.
| | - Francois Luro
- Unite Mixte de Recherche Amelioration Genetique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France.
| | - Grazia Maria Scarpa
- Dipartimento di AGRARIA Research Unit SACEG, University of Sassari, 07100 Sassari, Italy.
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Garavello M, Cuenca J, Dreissig S, Fuchs J, Houben A, Aleza P. Assessing Ploidy Level Analysis and Single Pollen Genotyping of Diploid and Euploid Citrus Genotypes by Fluorescence-Activated Cell Sorting and Whole-Genome Amplification. FRONTIERS IN PLANT SCIENCE 2019; 10:1174. [PMID: 31611896 PMCID: PMC6769063 DOI: 10.3389/fpls.2019.01174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/27/2019] [Indexed: 05/06/2023]
Abstract
Flow cytometry is widely used to determine genome size and ploidy level in plants. This technique, when coupled with fluorescence-activated cell sorting (FACS), whole genome amplification and genotyping (WGA), opens up new opportunities for genetic studies of individualized nuclei. This strategy was used to analyze the genetic composition of single pollen nuclei of different citrus species. The flow cytometry and microscope observations allowed us to differentiate the populations of pollen nuclei present in the diploid and euploid genotypes analyzed, showing that citrus has binuclear pollen. We have identified in the "CSO" tangor an additional nuclei population composed by the vegetative plus generative nuclei. Genotyping of this nuclei population revealed that vegetative and generative nuclei show the same genetic configuration. In addition, we have demonstrated the presence of unreduced gametes in the diploid genotype "Mexican lime." Genomic amplification is a robust method for haploid nuclei genotyping with several molecular markers, whereas in diploid nuclei using heterozygous markers showed a bias towards one of the two alleles, limiting the use of this tool in this type of nuclei. We further discuss the importance and applications of single pollen genotyping in citrus genetic studies.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- INTA, Concordia Agricultural Experiment Station, Concordia, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- *Correspondence: Pablo Aleza,
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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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Yu Y, Bai J, Chen C, Plotto A, Baldwin EA, Gmitter FG. Comparative analysis of juice volatiles in selected mandarins, mandarin relatives and other citrus genotypes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:1124-1131. [PMID: 28731231 DOI: 10.1002/jsfa.8563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Citrus fruit flavor is an important attribute prioritized in variety improvement. The present study compared juice volatiles compositions from 13 selected citrus genotypes, including six mandarins (Citrus reticulata), three sour oranges (Citrus aurantium), one blood orange (Citrus sinensis), one lime (Citrus limonia), one Clementine (Citrus clementina) and one satsuma (Citrus unshiu). RESULTS Large differences were observed with respect to volatile compositions among the citrus genotypes. 'Goutou' sour orange contained the greatest number of volatile compounds and the largest volatile production level. 'Ponkan' mandarin had the smallest number of volatiles and 'Owari' satsuma yielded the lowest volatile production level. 'Goutou' sour orange and 'Moro' blood orange were clearly distinguished from other citrus genotypes based on the analysis of volatile compositions, even though they were assigned into one single group with two other sour oranges by the molecular marker profiles. CONCLUSIONS The clustering analysis based on the aroma volatile compositions was able to differentiate mandarin varieties and natural sub-groups, and was also supported by the molecular marker study. The gas chromatography-mass spectrometry analysis of citrus juice aroma volatiles can be used as a tool to distinguish citrus genotypes and assist in the assessment of future citrus breeding programs. The aroma volatile profiles of the different citrus genotypes and inter-relationships detected among volatile compounds and among citrus genotypes will provide fundamental information on the development of marker-assisted selection in citrus breeding. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Yuan Yu
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
| | - Jinhe Bai
- Horticultural Research Laboratory, ARS, USDA, Fort Pierce, FL, USA
| | - Chunxian Chen
- Southeastern Fruit and Tree Nut Research Laboratory, ARS, USDA, Byron, GA, USA
| | - Anne Plotto
- Horticultural Research Laboratory, ARS, USDA, Fort Pierce, FL, USA
| | | | - Frederick G Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
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22
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Ndjiondjop MN, Semagn K, Zhang J, Gouda AC, Kpeki SB, Goungoulou A, Wambugu P, Dramé KN, Bimpong IK, Zhao D. Development of species diagnostic SNP markers for quality control genotyping in four rice ( Oryza L.) species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:131. [PMID: 30416368 PMCID: PMC6208651 DOI: 10.1007/s11032-018-0885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 05/04/2023]
Abstract
Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Kassa Semagn
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5 Canada
| | - Jianwei Zhang
- Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen Street, Tucson, AZ 85721 USA
| | - Arnaud Comlan Gouda
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Sèdjro Bienvenu Kpeki
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Alphonse Goungoulou
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Peterson Wambugu
- Kenya Agricultural and Livestock Research Organization (KALRO), Genetic Resources Research Institute, Nairobi, Kenya
| | | | - Isaac Kofi Bimpong
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Dule Zhao
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
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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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Andrello M, Henry K, Devaux P, Verdelet D, Desprez B, Manel S. Insights into the genetic relationships among plants of Beta section Beta using SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1857-1866. [PMID: 28589246 DOI: 10.1007/s00122-017-2929-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/30/2017] [Indexed: 05/23/2023]
Abstract
Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta. We analyzed the genetic variation of Beta section Beta, which includes wild taxa (Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables.
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Affiliation(s)
- Marco Andrello
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Karine Henry
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Pierre Devaux
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | | | - Bruno Desprez
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Stéphanie Manel
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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25
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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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26
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Wang X, Long Y, Wang N, Zou J, Ding G, Broadley MR, White PJ, Yuan P, Zhang Q, Luo Z, Liu P, Zhao H, Zhang Y, Cai H, King GJ, Xu F, Meng J, Shi L. Breeding histories and selection criteria for oilseed rape in Europe and China identified by genome wide pedigree dissection. Sci Rep 2017; 7:1916. [PMID: 28507329 PMCID: PMC5432491 DOI: 10.1038/s41598-017-02188-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/13/2017] [Indexed: 12/17/2022] Open
Abstract
Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees. IBD number and length were greater in the Ningyou7 pedigree than in the Tapidor pedigree. Seventy nine QTLs for flowering time, seed quality and root morphology traits were identified in the IBDs of Tapidor and Ningyou7. Many more candidate genes had been selected within the Ningyou7 pedigree than within the Tapidor pedigree. These results highlight differences in the transfer of favorable gene clusters controlling key traits during selection breeding in Europe and China.
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Affiliation(s)
- Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Biotechnology Research Institute, Chinese Academy of agricultural Science, Beijing, 100081, China
| | - Nian Wang
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
- King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pan Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Zhao
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China.
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27
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Butelli E, Garcia-Lor A, Licciardello C, Las Casas G, Hill L, Recupero GR, Keremane ML, Ramadugu C, Krueger R, Xu Q, Deng X, Fanciullino AL, Froelicher Y, Navarro L, Martin C. Changes in Anthocyanin Production during Domestication of Citrus. PLANT PHYSIOLOGY 2017; 173:2225-2242. [PMID: 28196843 PMCID: PMC5373055 DOI: 10.1104/pp.16.01701] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/10/2017] [Indexed: 05/17/2023]
Abstract
Mandarin (Citrus reticulata), citron (Citrus medica), and pummelo (Citrus maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of Citrus: sweet orange, sour orange, clementine, lemon, lime, and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not, and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars. A white mutant of lemon lacks functional alleles of Ruby, demonstrating that Ruby plays an essential role in anthocyanin production in Citrus Almost all the natural variation in pigmentation by anthocyanins in Citrus species can be explained by differences in activity of the Ruby gene, caused by point mutations and deletions and insertions of transposable elements. Comparison of the allelic constitution of Ruby in different species and cultivars also helps to clarify many of the taxonomic relationships in different species of Citrus, confirms the derivation of commercial varieties during domestication, elucidates the relationships within the subgenus Papeda, and allows a new genetic classification of mandarins.
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Affiliation(s)
- Eugenio Butelli
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.);
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.);
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.);
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.);
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.);
- University of California, Riverside, California 92521 (C.R.);
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.);
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Andrés Garcia-Lor
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Concetta Licciardello
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Giuseppina Las Casas
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Lionel Hill
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Giuseppe Reforgiato Recupero
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Manjunath L Keremane
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Chandrika Ramadugu
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Robert Krueger
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Qiang Xu
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Xiuxin Deng
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Anne-Laure Fanciullino
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Yann Froelicher
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Luis Navarro
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Cathie Martin
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
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A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin. Forensic Sci Int Genet 2017; 27:132-141. [DOI: 10.1016/j.fsigen.2016.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 11/20/2022]
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Penjor T, Mimura T, Kotoda N, Matsumoto R, Nagano AJ, Honjo MN, Kudoh H, Yamamoto M, Nagano Y. RAD-Seq analysis of typical and minor Citrus accessions, including Bhutanese varieties. BREEDING SCIENCE 2016; 66:797-807. [PMID: 28163596 PMCID: PMC5282754 DOI: 10.1270/jsbbs.16059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/11/2016] [Indexed: 05/30/2023]
Abstract
We analyzed the reduced-representation genome sequences of Citrus species by double-digest restriction site-associated DNA sequencing (ddRAD-Seq) using 44 accessions, including typical and minor accessions, such as Bhutanese varieties. The results of this analysis using typical accessions were consistent with previous reports that citron, papeda, pummelo, and mandarin are ancestral species, and that most Citrus species are derivatives or hybrids of these four species. Citrus varieties often reproduce asexually and heterozygosity is highly conserved within each variety. Because this approach could readily detect conservation of heterozygosity, it was able to discriminate citrus varieties such as satsuma mandarin from closely related species. Thus, this method provides an inexpensive way to protect citrus varieties from unintended introduction and to prevent the provision of incorrect nursery stocks to customers. One Citrus variety in Bhutan was morphologically similar to Mexican lime and was designated as Himalayan lime. The current analysis confirmed the previous proposition that Mexican lime is a hybrid between papeda and citron, and also suggested that Himalayan lime is a probable hybrid between mandarin and citron. In addition to Himalayan lime, current analysis suggested that several accessions were formed by previously undescribed combinations.
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Affiliation(s)
- Tshering Penjor
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
- Renewable Natural Resources Research Centre Wengkhar,
Mongar,
Bhutan
| | - Takashi Mimura
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Nobuhiro Kotoda
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Ryoji Matsumoto
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Atsushi J. Nagano
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
- JST PRESTO,
4-1-8, Honcho, Kawaguchi, Saitama 332-0012,
Japan
- Faculty of Agriculture, Ryukoku University,
1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194,
Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
| | - Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University,
1-21-35 Korimoto, Kagoshima 890-0065,
Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
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Stočes Š, Ruttink T, Bartoš J, Studer B, Yates S, Zwierzykowski Z, Abrouk M, Roldán-Ruiz I, Książczyk T, Rey E, Doležel J, Kopecký D. Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery. THE PLANT GENOME 2016; 9. [PMID: 27902806 DOI: 10.3835/plantgenome2016.02.0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively. In addition, we used transcriptome sequence data of perennial ryegrass ( L.) from a previous study to identify 16,613 transcripts shared across all three species. Large numbers of intraspecific SNPs were identified in all three species: 248,000 in meadow fescue, 715,000 in Italian ryegrass, and 529,000 in perennial ryegrass. Moreover, we identified almost 25,000 interspecific SNPs located in 5343 genes that can distinguish meadow fescue from Italian ryegrass and 15,000 SNPs located in 3976 genes that discriminate meadow fescue from both species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of using the GenomeZipper approach. With the identification and positioning of interspecific SNPs, our study provides a valuable resource for the grass research and breeding community and will enable detailed characterization of genomic composition and gene expression analysis in prospective × hybrids.
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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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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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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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