A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes
Background Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2015
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/65052 |
| _version_ | 1855522488949145600 |
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| author | Soto, Johana Carolina Ortíz, Juan Felipe Perlaza-Jiménez, Laura Vásquez, Andrea Ximena Becerra López Lavelle, Luis Augusto Mathew, Boby Léon, Jens Bernal, Adriana Jimena Ballvora, Agim López Carrascal, Camilo Ernesto |
| author_browse | Ballvora, Agim Becerra López Lavelle, Luis Augusto Bernal, Adriana Jimena Léon, Jens López Carrascal, Camilo Ernesto Mathew, Boby Ortíz, Juan Felipe Perlaza-Jiménez, Laura Soto, Johana Carolina Vásquez, Andrea Ximena |
| author_facet | Soto, Johana Carolina Ortíz, Juan Felipe Perlaza-Jiménez, Laura Vásquez, Andrea Ximena Becerra López Lavelle, Luis Augusto Mathew, Boby Léon, Jens Bernal, Adriana Jimena Ballvora, Agim López Carrascal, Camilo Ernesto |
| author_sort | Soto, Johana Carolina |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.
Results
A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.
Conclusions
This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium. |
| format | Journal Article |
| id | CGSpace65052 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace650522025-03-13T09:44:09Z A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes Soto, Johana Carolina Ortíz, Juan Felipe Perlaza-Jiménez, Laura Vásquez, Andrea Ximena Becerra López Lavelle, Luis Augusto Mathew, Boby Léon, Jens Bernal, Adriana Jimena Ballvora, Agim López Carrascal, Camilo Ernesto chromosome mapping genetic maps manihot esculenta crantz dna genes genetic markers polymorphism mapas genéticos adn marcadores genéticos polimorfismo Background Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. Results A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. Conclusions This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium. 2015-12 2015-04-07T14:42:21Z 2015-04-07T14:42:21Z Journal Article https://hdl.handle.net/10568/65052 en Open Access Springer Soto, Johana Carolina; Ortiz, Juan Felipe; Perlaza-Jiménez, Laura; Vásquez, Andrea Ximena; Becerra López-Lavalle, Luis Augusto; Mathew, Boby; Léon, Jens; Bernal, Adriana Jimena; Ballvora, Agim; López, Camilo Ernesto. 2015. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics 16:190. |
| spellingShingle | chromosome mapping genetic maps manihot esculenta crantz dna genes genetic markers polymorphism mapas genéticos adn marcadores genéticos polimorfismo Soto, Johana Carolina Ortíz, Juan Felipe Perlaza-Jiménez, Laura Vásquez, Andrea Ximena Becerra López Lavelle, Luis Augusto Mathew, Boby Léon, Jens Bernal, Adriana Jimena Ballvora, Agim López Carrascal, Camilo Ernesto A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes |
| title | A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes |
| title_full | A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes |
| title_fullStr | A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes |
| title_full_unstemmed | A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes |
| title_short | A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes |
| title_sort | genetic map of cassava manihot esculenta crantz with integrated physical mapping of immunity related genes |
| topic | chromosome mapping genetic maps manihot esculenta crantz dna genes genetic markers polymorphism mapas genéticos adn marcadores genéticos polimorfismo |
| url | https://hdl.handle.net/10568/65052 |
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