A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping
Background: Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The ava...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | article |
| Language: | Inglés |
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2017
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| Online Access: | http://hdl.handle.net/20.500.11939/4245 |
| _version_ | 1855032089014960128 |
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| author | Ollitrault, Patrick Terol, Javier Chen, Chunxian Federici, Claire T. Lotfy, Samia Hippolyte, Isabelle Ollitrault, Frederique Berard, Aurelie Chauveau, Aurelie Cuenca, José Costantino, Gilles Kacar, Yildiz Aka Mu, Lisa García-Lor, Andrés Froelicher, Yann Aleza, Pablo Boland, Anne Billot, Claire Navarro, Luis Luro, Francois Roose, Mikeal L. Gmitter Jr., Frederick G. Talón, Manuel Brunel, Dominique |
| author_browse | Aleza, Pablo Berard, Aurelie Billot, Claire Boland, Anne Brunel, Dominique Chauveau, Aurelie Chen, Chunxian Costantino, Gilles Cuenca, José Federici, Claire T. Froelicher, Yann García-Lor, Andrés Gmitter Jr., Frederick G. Hippolyte, Isabelle Kacar, Yildiz Aka Lotfy, Samia Luro, Francois Mu, Lisa Navarro, Luis Ollitrault, Frederique Ollitrault, Patrick Roose, Mikeal L. Talón, Manuel Terol, Javier |
| author_facet | Ollitrault, Patrick Terol, Javier Chen, Chunxian Federici, Claire T. Lotfy, Samia Hippolyte, Isabelle Ollitrault, Frederique Berard, Aurelie Chauveau, Aurelie Cuenca, José Costantino, Gilles Kacar, Yildiz Aka Mu, Lisa García-Lor, Andrés Froelicher, Yann Aleza, Pablo Boland, Anne Billot, Claire Navarro, Luis Luro, Francois Roose, Mikeal L. Gmitter Jr., Frederick G. Talón, Manuel Brunel, Dominique |
| author_sort | Ollitrault, Patrick |
| collection | ReDivia |
| description | Background: Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin x sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results: Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions: A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. |
| format | article |
| id | ReDivia4245 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia42452025-04-25T14:42:38Z A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping Ollitrault, Patrick Terol, Javier Chen, Chunxian Federici, Claire T. Lotfy, Samia Hippolyte, Isabelle Ollitrault, Frederique Berard, Aurelie Chauveau, Aurelie Cuenca, José Costantino, Gilles Kacar, Yildiz Aka Mu, Lisa García-Lor, Andrés Froelicher, Yann Aleza, Pablo Boland, Anne Billot, Claire Navarro, Luis Luro, Francois Roose, Mikeal L. Gmitter Jr., Frederick G. Talón, Manuel Brunel, Dominique Background: Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin x sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results: Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions: A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. 2017-06-01T10:09:40Z 2017-06-01T10:09:40Z 2012 NOV 5 2012 article publishedVersion Ollitrault, P., Terol, J., Chen, C., Federici, C. T., Lotfy, S., Hippolyte, I., ... & Costantino, G. (2012). A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC genomics, 13(1), 593. 1471-2164 http://hdl.handle.net/20.500.11939/4245 10.1186/1471-2164-13-593 en openAccess Impreso |
| spellingShingle | Ollitrault, Patrick Terol, Javier Chen, Chunxian Federici, Claire T. Lotfy, Samia Hippolyte, Isabelle Ollitrault, Frederique Berard, Aurelie Chauveau, Aurelie Cuenca, José Costantino, Gilles Kacar, Yildiz Aka Mu, Lisa García-Lor, Andrés Froelicher, Yann Aleza, Pablo Boland, Anne Billot, Claire Navarro, Luis Luro, Francois Roose, Mikeal L. Gmitter Jr., Frederick G. Talón, Manuel Brunel, Dominique A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping |
| title | A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping |
| title_full | A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping |
| title_fullStr | A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping |
| title_full_unstemmed | A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping |
| title_short | A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping |
| title_sort | reference genetic map of c clementina hort ex tan citrus evolution inferences from comparative mapping |
| url | http://hdl.handle.net/20.500.11939/4245 |
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