Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus
Introduction: Useful germplasm for citrus breeding includes all sexually compatible species of the former genera Citrus, Clymenia, Eremocitrus, Fortunella, Microcitrus, Oxanthera, and Poncirus, now merged in the single Citrus genus. An improved knowledge on the synteny/collinearity between the g...
| Autores principales: | , , , , , , , , , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers
2025
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.11939/9024 https://www.frontiersin.org/articles/10.3389/fpls.2024.1475965/ |
| _version_ | 1855492609266417664 |
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| author | Ollitrault, Patrick Hufnagel, Barbara Curk, Franck Perdereau, Aude Mournet, Pierre Maëva, Miranda Constantino, Guilles Froelicher, Yann Alves, Monica Forner-Giner, María A. Wesley Smith, Malcolm Aleza, Pablo Luro, Francois Wulf, Nelson A. Pena, Leandro Morillon, Raphael Lemainque, Arnaud |
| author_browse | Aleza, Pablo Alves, Monica Constantino, Guilles Curk, Franck Forner-Giner, María A. Froelicher, Yann Hufnagel, Barbara Lemainque, Arnaud Luro, Francois Maëva, Miranda Morillon, Raphael Mournet, Pierre Ollitrault, Patrick Pena, Leandro Perdereau, Aude Wesley Smith, Malcolm Wulf, Nelson A. |
| author_facet | Ollitrault, Patrick Hufnagel, Barbara Curk, Franck Perdereau, Aude Mournet, Pierre Maëva, Miranda Constantino, Guilles Froelicher, Yann Alves, Monica Forner-Giner, María A. Wesley Smith, Malcolm Aleza, Pablo Luro, Francois Wulf, Nelson A. Pena, Leandro Morillon, Raphael Lemainque, Arnaud |
| author_sort | Ollitrault, Patrick |
| collection | ReDivia |
| description | Introduction: Useful germplasm for citrus breeding includes all sexually
compatible species of the former genera Citrus, Clymenia, Eremocitrus,
Fortunella, Microcitrus, Oxanthera, and Poncirus, now merged in the single
Citrus genus. An improved knowledge on the synteny/collinearity between the
genome of these different species, and on their recombination landscapes, is
essential to optimize interspecific breeding schemes.
Method: We have performed a large comparative genetic mapping study
including several main clades of the Citrus genus. It concerns five species
(C. maxima, C. medica, C. reticulata, C. trifoliata and C. glauca), twoC. maxima x C. reticulata). The nine individual genetic maps were established
from GBS data of 1,216 hybrids.
Results and discussion: The number of SNPs mapped for each parent varies from
760 for C. medica to 4,436 for the C. maxima x C. reticulata hybrid, with an
average of 2,162.3 markers by map. Their comparison with C. clementina v1.0
assembly and inter-map comparisons revealed a high synteny and collinearity
between the nine genetic maps. Non-Mendelian segregation was frequent and
specific for each parental combination. The recombination landscape was similar
for the nine mapped parents, and large genomic regions with very low
recombination were identified. A consensus genetic map was successfully
established. It encompasses 10,756 loci, including 7,915 gene-based markers
and 2,841 non-genic SNPs. The anchoring of the consensus map on 15 published
citrus chromosome-scale genome assemblies revealed a high synteny and
collinearity for the most recent assemblies, whereas discrepancies were
observed for some older ones. Large structural variations do not seem to have
played a major role in the differentiation of the main species of the Citrus genus.
The consensus genetic map is a useful tool to check the accuracy of genome
assemblies, identify large structural variation and focus on analyzing potential
relationships with phenotypic variations. It should also be a reference framework
to integrate the positions of QTLs and useful genes identified in different analyses
horticultural groups resulting from interspecific admixture (clementine and
lemon) and two recent interspecific hybrids (C. australis x C. australasica and |
| format | Artículo |
| id | ReDivia9024 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Frontiers |
| publisherStr | Frontiers |
| record_format | dspace |
| spelling | ReDivia90242025-04-25T14:49:47Z Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus Ollitrault, Patrick Hufnagel, Barbara Curk, Franck Perdereau, Aude Mournet, Pierre Maëva, Miranda Constantino, Guilles Froelicher, Yann Alves, Monica Forner-Giner, María A. Wesley Smith, Malcolm Aleza, Pablo Luro, Francois Wulf, Nelson A. Pena, Leandro Morillon, Raphael Lemainque, Arnaud Citrus Genetic map comparison Genotyping by sequencing Comparative genomic analysis Recombination landscape Skewed segregation Introduction: Useful germplasm for citrus breeding includes all sexually compatible species of the former genera Citrus, Clymenia, Eremocitrus, Fortunella, Microcitrus, Oxanthera, and Poncirus, now merged in the single Citrus genus. An improved knowledge on the synteny/collinearity between the genome of these different species, and on their recombination landscapes, is essential to optimize interspecific breeding schemes. Method: We have performed a large comparative genetic mapping study including several main clades of the Citrus genus. It concerns five species (C. maxima, C. medica, C. reticulata, C. trifoliata and C. glauca), twoC. maxima x C. reticulata). The nine individual genetic maps were established from GBS data of 1,216 hybrids. Results and discussion: The number of SNPs mapped for each parent varies from 760 for C. medica to 4,436 for the C. maxima x C. reticulata hybrid, with an average of 2,162.3 markers by map. Their comparison with C. clementina v1.0 assembly and inter-map comparisons revealed a high synteny and collinearity between the nine genetic maps. Non-Mendelian segregation was frequent and specific for each parental combination. The recombination landscape was similar for the nine mapped parents, and large genomic regions with very low recombination were identified. A consensus genetic map was successfully established. It encompasses 10,756 loci, including 7,915 gene-based markers and 2,841 non-genic SNPs. The anchoring of the consensus map on 15 published citrus chromosome-scale genome assemblies revealed a high synteny and collinearity for the most recent assemblies, whereas discrepancies were observed for some older ones. Large structural variations do not seem to have played a major role in the differentiation of the main species of the Citrus genus. The consensus genetic map is a useful tool to check the accuracy of genome assemblies, identify large structural variation and focus on analyzing potential relationships with phenotypic variations. It should also be a reference framework to integrate the positions of QTLs and useful genes identified in different analyses horticultural groups resulting from interspecific admixture (clementine and lemon) and two recent interspecific hybrids (C. australis x C. australasica and 2025-02-12T10:59:01Z 2025-02-12T10:59:01Z 2024 article publishedVersion Ollitrault, P., Hufnagel, B., Curk, F., Perdereau, A., Mournet, P., Miranda, M., ... & Lemainque, A. (2024). Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus. Frontiers in Plant Science, 15, 1475965. 1664-462X https://hdl.handle.net/20.500.11939/9024 10.3389/fpls.2024.1475965 https://www.frontiersin.org/articles/10.3389/fpls.2024.1475965/ en The author(s) declare financial support was received for the research, authorship, and/or publication of this article.This research was funded by France Génomique (ANR-10-INBS-09–08; “Dynamo” project), European Feder-Guadeloupe region “Cavalbio” project, H2020 Innovation Action Program (grant #817526, preHLB project), French National Research Agency (grant ANR-23-CE20-0038), Ministry of Science and Innovation Spain (project PID2021-1281150R-I00), MCIN/AEI/10.13039/ 501100011033/FEDER, UE., and Hort. Innovation, Australia. info:eu-repo/grantAgreement/EC/H2020/817526/EU/Preventing HLB epidemics for ensuring citrus survival in Europe/PRE-HLB Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ openAccess Frontiers electronico |
| spellingShingle | Citrus Genetic map comparison Genotyping by sequencing Comparative genomic analysis Recombination landscape Skewed segregation Ollitrault, Patrick Hufnagel, Barbara Curk, Franck Perdereau, Aude Mournet, Pierre Maëva, Miranda Constantino, Guilles Froelicher, Yann Alves, Monica Forner-Giner, María A. Wesley Smith, Malcolm Aleza, Pablo Luro, Francois Wulf, Nelson A. Pena, Leandro Morillon, Raphael Lemainque, Arnaud Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus |
| title | Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus |
| title_full | Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus |
| title_fullStr | Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus |
| title_full_unstemmed | Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus |
| title_short | Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus |
| title_sort | comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the citrus genus |
| topic | Citrus Genetic map comparison Genotyping by sequencing Comparative genomic analysis Recombination landscape Skewed segregation |
| url | https://hdl.handle.net/20.500.11939/9024 https://www.frontiersin.org/articles/10.3389/fpls.2024.1475965/ |
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