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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. PLANTS (BASEL, SWITZERLAND) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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2
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Aleza P, Garavello MF, Rouiss H, Benedict AC, Garcia-Lor A, Hernández M, Navarro L, Ollitrault P. Inheritance pattern of tetraploids pummelo, mandarin, and their interspecific hybrid sour orange is highly influenced by their phylogenomic structure. FRONTIERS IN PLANT SCIENCE 2023; 14:1327872. [PMID: 38143579 PMCID: PMC10739408 DOI: 10.3389/fpls.2023.1327872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Citrus polyploidy is associated with a wide range of morphological, genetic, and physiological changes that are often advantageous for breeding. Citrus triploid hybrids are very interesting as new seedless varieties. However, tetraploid rootstocks promote adaptation to different abiotic stresses and promote resilience. Triploid and tetraploid hybrids can be obtained through sexual hybridizations using tetraploid parents (2x × 4x, 4x × 2x, or 4x × 4x), but more knowledge is needed about the inheritance pattern of tetraploid parents to optimize the efficiency of triploid varieties and tetraploid rootstock breeding strategies. In this work, we have analyzed the inheritance pattern of three tetraploid genotypes: 'Chandler' pummelo (Citrus maxima) and 'Cleopatra' mandarin (Citrus reticulata), which represent two clear examples of autotetraploid plants constituted by the genome of a single species, and the 'Sevillano' sour orange, which is an allotetraploid interspecific hybrid between C. maxima and C. reticulata. Polymorphic simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers were used to estimate parental heterozygosity restitution, and allele frequencies for centromeric loci were used to calculate the preferential pairing rate related to the proportion of disomic and tetrasomic segregation. The tetraploid pummelo and mandarin displayed tetrasomic segregation. Sour orange evidenced a clear intermediate inheritance for five of the nine chromosomes (1, 2, 5, 7, and 8), a slight tendency toward tetrasomic inheritance on chromosome 3, and intermediate inheritance with a tendency toward disomy for chromosomes 4, 6, and 9. These results indicate that the interspecific versus intraspecific phylogenomic origin affects preferential pairing and, therefore, the inheritance patterns. Despite its high level of heterozygosity, the important preferential chromosome pairing observed in sour orange results in a limited diversity of the genotypic variability of its diploid gametes, and consequently, a large part of the genetic value of the original diploid sour orange is transferred to the tetraploid progenies.
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Affiliation(s)
- Pablo Aleza
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Miguel Fernando Garavello
- Concordia Agricultural Experimental Station, National Agricultural Technology Institute, Concordia, Entre Ríos, Argentina
| | - Houssem Rouiss
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Ana Cristina Benedict
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Andres Garcia-Lor
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Maria Hernández
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Luis Navarro
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Patrick Ollitrault
- Centre de coopération internationale en recherche agronomique pour le développement Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (UMR AGAP) Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), INRAE, Institut Agro, Montpellier, France
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3
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Ferrer V, Costantino G, Paymal N, Quinton C, Perdomo EC, Paoli M, Mournet P, Ollitrault P, Tomi F, Luro F. Inheritance and Quantitative Trait Loci Mapping of Aromatic Compounds from Clementine ( Citrus × clementina Hort. ex Tan.) and Sweet Orange ( C. × sinensis (L.) Osb.) Fruit Essential Oils. Genes (Basel) 2023; 14:1800. [PMID: 37761942 PMCID: PMC10531275 DOI: 10.3390/genes14091800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Despite their importance in food processing, perfumery and cosmetics, the inheritance of sweet orange aromatic compounds, as well as their yield in the fruit peel, has been little analyzed. In the present study, the segregation of aromatic compounds was studied in an F1 population of 77 hybrids resulting from crosses between clementine and blood sweet orange. Fruit-peel essential oils (PEOs) extracted by hydrodistillation were analyzed by gas chromatography coupled with flame ionization detection. Genotyping by sequencing was performed on the parents and the hybrids. The resulting "clementine × sweet blood orange" genetic map consists of 710 SNP markers distributed in nine linkage groups (LGs), representing the nine citrus chromosomes, and spanning 1054 centimorgans. Twenty quantitative trait loci (QTLs) were identified, explaining between 20.5 and 55.0% of the variance of the major aromatic compounds and PEO yield. The QTLs for monoterpenes and aliphatic aldehydes predominantly colocalized on LGs 5 and 8, as did the two QTLs for PEO yield. The sesquiterpene QTLs were located on LGs 1, 3, 6 and 8. The detection of major QTLs associated with the synthesis of aliphatic aldehydes, known for their strong aromatic properties, open the way for marker-assisted selection.
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Affiliation(s)
- Vincent Ferrer
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France; (V.F.); (G.C.); (E.C.P.)
- Rémy Cointreau—Les Molières, 49124 Saint-Barthélemy-d’Anjou, France; (N.P.); (C.Q.)
| | - Gilles Costantino
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France; (V.F.); (G.C.); (E.C.P.)
| | - Noémie Paymal
- Rémy Cointreau—Les Molières, 49124 Saint-Barthélemy-d’Anjou, France; (N.P.); (C.Q.)
| | - Carole Quinton
- Rémy Cointreau—Les Molières, 49124 Saint-Barthélemy-d’Anjou, France; (N.P.); (C.Q.)
| | - Estefania Carrillo Perdomo
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France; (V.F.); (G.C.); (E.C.P.)
| | - Mathieu Paoli
- UMR SPE 6134—Université de Corse—CNRS, 20000 Ajaccio, France; (M.P.); (F.T.)
| | - Pierre Mournet
- CIRAD, UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France;
| | - Patrick Ollitrault
- CIRAD, UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France;
| | - Félix Tomi
- UMR SPE 6134—Université de Corse—CNRS, 20000 Ajaccio, France; (M.P.); (F.T.)
| | - François Luro
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France; (V.F.); (G.C.); (E.C.P.)
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Jabeen S, Saif R, Haq R, Hayat A, Naz S. Whole-genome sequencing and variant discovery of Citrus reticulata "Kinnow" from Pakistan. Funct Integr Genomics 2023; 23:227. [PMID: 37422603 DOI: 10.1007/s10142-023-01153-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/10/2023]
Abstract
Citrus is a source of nutritional and medicinal advantages, cultivated worldwide with major groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars Feutral's Early, Dancy, Honey, and Kinnow. The present study designed to understand the genetic architecture of this unique variety of Citrus reticulata 'Kinnow.' The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seedlessness, juice content, thickness of peel, and shelf-life. A total of 139,436,350 raw sequence reads were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, 3,503,033 SNPs, 176,949 MNPs, 323,287 INS, and 333,083 DEL were identified using the GATK4 variant calling pipeline against Citrus clementina. Furthermore, g:Profiler was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts in cellular components. In a nutshell, 18,153 high impact variants and 216 genic variants found in the current study, which may be used after its functional validation for marker-assisted breeding programs of "Kinnow" to propagate its valued traits for the improvement of contemporary citrus varieties in the region.
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Affiliation(s)
- Sadia Jabeen
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Rashid Saif
- Department of Biotechnology, Qarshi University, Lahore, Pakistan
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
| | - Rukhama Haq
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Akbar Hayat
- Citrus Research Institute, Sargodha, Pakistan
| | - Shagufta Naz
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan.
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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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6
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Calvez L, Dereeper A, Perdereau A, Mournet P, Miranda M, Bruyère S, Hufnagel B, Froelicher Y, Lemainque A, Morillon R, Ollitrault P. Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks. PLANTS (BASEL, SWITZERLAND) 2023; 12:1630. [PMID: 37111854 PMCID: PMC10146282 DOI: 10.3390/plants12081630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Sexual breeding at the tetraploid level is a promising strategy for rootstock breeding in citrus. Due to the interspecific origin of most of the conventional diploid citrus rootstocks that produced the tetraploid germplasm, the optimization of this strategy requires better knowledge of the meiotic behavior of the tetraploid parents. This work used Genotyping By Sequencing (GBS) data from 103 tetraploid hybrids to study the meiotic behavior and generate a high-density recombination landscape for their tetraploid intergenic Swingle citrumelo and interspecific Volkamer lemon progenitors. A genetic association study was performed with root architecture traits. For citrumelo, high preferential chromosome pairing was revealed and led to an intermediate inheritance with a disomic tendency. Meiosis in Volkamer lemon was more complex than that of citrumelo, with mixed segregation patterns from disomy to tetrasomy. The preferential pairing resulted in low interspecific recombination levels and high interspecific heterozygosity transmission by the diploid gametes. This meiotic behavior affected the efficiency of Quantitative Trait Loci (QTL) detection. Nevertheless, it enabled a high transmission of disease and pest resistance candidate genes from P. trifoliata that are heterozygous in the citrumelo progenitor. The tetrazyg strategy, using doubled diploids of interspecific origin as parents, appears to be efficient in transferring the dominant traits selected at the parental level to the tetraploid progenies.
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Affiliation(s)
- Lény Calvez
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Alexis Dereeper
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Aude Perdereau
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France; (A.P.)
| | - Pierre Mournet
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Maëva Miranda
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Saturnin Bruyère
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Barbara Hufnagel
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Yann Froelicher
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-20230 San Giuliano, France
| | - Arnaud Lemainque
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France; (A.P.)
| | - Raphaël Morillon
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Patrick Ollitrault
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
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Montalt R, Cuenca J, Vives MC, Mournet P, Navarro L, Ollitrault P, Aleza P. Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus. PLANTS (BASEL, SWITZERLAND) 2023; 12:1567. [PMID: 37050193 PMCID: PMC10096700 DOI: 10.3390/plants12071567] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Polyembryony and male sterility (MS) are essential characters for citrus breeding. MS, coupled with parthenocarpy, allows for addressing the diversification of diploid seedless mandarin varieties, and nucleocytoplasmic MS is the most prevalent system. Polyembryony limits the use of seed parents in scion breeding programs, and the recovery of monoembryonic hybrids to be used as female parents is a crucial pre-breeding component. The objectives of this work were the identification of SNPs closely linked with the genes implied in these traits for marker-assisted selection. Genotyping by sequencing was used to genotype 61 diploid hybrids from an F1 progeny recovered from crossing 'Kiyomi' and 'Murcott' tangors. A total of 6444 segregating markers were identified and used to establish the two parental genetic maps. They consisted of 1374 and 697 markers encompassing 1416.287 and 1339.735 cM for 'Kiyomi' and 'Murcott', respectively. Phenotyping for MS and polyembryony was performed. The genotype-trait association study identified a genomic region on LG8 which was significantly associated with MS, and a genomic region on LG1 which was significantly associated with polyembryony. Annotation of the identified region for MS revealed 19 candidate genes. One SNP KASPar marker was developed and fully validated for each trait.
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Affiliation(s)
- Rafael Montalt
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain
| | - José Cuenca
- Agrupación de Viveristas de Agrios (AVASA), 12570 Castellón, Spain
| | - María Carmen Vives
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain
| | - Pierre Mournet
- UMR AGAP, CIRAD, 34398 Montpellier, France
- UMR AGAP, Institut Agro, CIRAD, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain
| | - Patrick Ollitrault
- UMR AGAP, CIRAD, 34398 Montpellier, France
- UMR AGAP, Institut Agro, CIRAD, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain
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8
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Alves MN, Raiol-Junior LL, Girardi EA, Miranda M, Wulff NA, Carvalho EV, Lopes SA, Ferro JA, Ollitrault P, Peña L. Insight into resistance to ' Candidatus Liberibacter asiaticus,' associated with Huanglongbing, in Oceanian citrus genotypes. FRONTIERS IN PLANT SCIENCE 2022; 13:1009350. [PMID: 36160987 PMCID: PMC9500433 DOI: 10.3389/fpls.2022.1009350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
Huanglongbing (HLB), the most destructive citrus disease, is associated with unculturable, phloem-limited Candidatus Liberibacter species, mainly Ca. L. asiaticus (Las). Las is transmitted naturally by the insect Diaphorina citri. In a previous study, we determined that the Oceanian citrus relatives Eremocitrus glauca, Microcitrus warburgiana, Microcitrus papuana, and Microcitrus australis and three hybrids among them and Citrus were full-resistant to Las. After 2 years of evaluations, leaves of those seven genotypes remained Las-free even with their susceptible rootstock being infected. However, Las was detected in their stem bark above the scion-rootstock graft union. Aiming to gain an understanding of the full-resistance phenotype, new experiments were carried out with the challenge-inoculated Oceanian citrus genotypes through which we evaluated: (1) Las acquisition by D. citri fed onto them; (2) Las infection in sweet orange plants grafted with bark or budwood from them; (3) Las infection in sweet orange plants top-grafted onto them; (4) Las infection in new shoots from rooted plants of them; and (5) Las infection in new shoots of them after drastic back-pruning. Overall, results showed that insects that fed on plants from the Oceanian citrus genotypes, their canopies, new flushes, and leaves from rooted cuttings evaluated remained quantitative real-time polymerase chain reaction (qPCR)-negative. Moreover, their budwood pieces were unable to infect sweet orange through grafting. Furthermore, sweet orange control leaves resulted infected when insects fed onto them and graft-receptor susceptible plants. Genomic and morphological analysis of the Oceanian genotypes corroborated that E. glauca and M. warburgiana are pure species while our M. australis accession is an M. australis × M. inodora hybrid and M. papuana is probably a M. papuana × M. warburgiana hybrid. E. glauca × C. sinensis hybrid was found coming from a cross between E. glauca and mandarin or tangor. Eremocitrus × Microcitrus hybrid is a complex admixture of M. australasica, M. australis, and E. glauca while the last hybrid is an M. australasica × M. australis admixture. Confirmation of consistent full resistance in these genotypes with proper validation of their genomic parentages is essential to map properly genomic regions for breeding programs aimed to generate new Citrus-like cultivars yielding immunity to HLB.
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Affiliation(s)
- Mônica N. Alves
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Laudecir L. Raiol-Junior
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Empresa Brasileira de Pesquisa Agropecuária, Cruz das Almas, Brazil
| | - Eduardo A. Girardi
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Empresa Brasileira de Pesquisa Agropecuária, Cruz das Almas, Brazil
| | - Maéva Miranda
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Everton V. Carvalho
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Empresa Brasileira de Pesquisa Agropecuária, Cruz das Almas, Brazil
| | | | - Jesus A. Ferro
- Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Patrick Ollitrault
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Leandro Peña
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Instituto de Biologia Molecular y Celular de Plantas – Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
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9
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Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC PLANT BIOLOGY 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
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Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Brottier L, Chaintreuil C, Simion P, Scornavacca C, Rivallan R, Mournet P, Moulin L, Lewis GP, Fardoux J, Brown SC, Gomez-Pacheco M, Bourges M, Hervouet C, Gueye M, Duponnois R, Ramanankierana H, Randriambanona H, Vandrot H, Zabaleta M, DasGupta M, D’Hont A, Giraud E, Arrighi JF. A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses. BMC PLANT BIOLOGY 2018; 18:333. [PMID: 30518342 PMCID: PMC6282307 DOI: 10.1186/s12870-018-1567-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene. RESULTS This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity. CONCLUSIONS The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.
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Affiliation(s)
- Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Paul Simion
- Institut des Sciences de l’Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Cedex 5 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Cedex 5 Montpellier, France
| | - Ronan Rivallan
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Pierre Mournet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Lionel Moulin
- IRD, Interactions Plantes Microorganismes Environnement, UMR IPME, 34394 Montpellier, France
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB UK
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Spencer C. Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mario Gomez-Pacheco
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourges
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Catherine Hervouet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Mathieu Gueye
- Laboratoire de Botanique, Institut Fondamental d’Afrique Noire, Ch. A. Diop, BP 206 Dakar, Sénégal
| | - Robin Duponnois
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Hervé Vandrot
- IAC, Laboratoire de Botanique et d’Ecologie Végétale Appliquée, UMR AMAP, 98825 Pouembout, Nouvelle-Calédonie France
| | - Maria Zabaleta
- Department of Biochemistry and Microbial Genomics, IIBCE, 11600 Montevideo, Uruguay
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019 India
| | - Angélique D’Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
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17
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Chávez-Dulanto PN, Rey B, Ubillús C, Rázuri V, Bazán R, Sarmiento J. Foliar application of macro- and micronutrients for pest-mites control in citrus crops. Food Energy Secur 2018. [DOI: 10.1002/fes3.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Benjamín Rey
- Servicios Especiales de Formulación Industrial SERFI; Lima Peru
| | | | | | - Rubén Bazán
- Faculty of Agronomy; Universidad Nacional Agraria La Molina; Lima Peru
| | - Jorge Sarmiento
- Faculty of Agronomy; Universidad Nacional Agraria La Molina; Lima Peru
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