A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

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cg.creator.identifierLuis Augusto Becerra Lopez-Lavalle: 0000-0003-3520-2270
cg.identifier.doihttps://doi.org/10.1186/s12864-015-1397-4en
cg.isijournalISI Journalen
cg.issn1471-2164en
cg.issue1en
cg.journalBMC Genomicsen
cg.subject.ciatCASSAVAen
cg.subject.ciatGENETIC RESOURCESen
cg.volume16en
dc.contributor.authorSoto, Johana Carolinaen
dc.contributor.authorOrtíz, Juan Felipeen
dc.contributor.authorPerlaza-Jiménez, Lauraen
dc.contributor.authorVásquez, Andrea Ximenaen
dc.contributor.authorBecerra López Lavelle, Luis Augustoen
dc.contributor.authorMathew, Bobyen
dc.contributor.authorLéon, Jensen
dc.contributor.authorBernal, Adriana Jimenaen
dc.contributor.authorBallvora, Agimen
dc.contributor.authorLópez Carrascal, Camilo Ernestoen
dc.date.accessioned2015-04-07T14:42:21Zen
dc.date.available2015-04-07T14:42:21Zen
dc.identifier.urihttps://hdl.handle.net/10568/65052
dc.titleA genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genesen
dcterms.abstractBackground 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.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2015-03-16
dcterms.bibliographicCitationSoto, 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.en
dcterms.descriptionCIAT- Outstanding Research Publication Award (ORPA) - 2015en
dcterms.issued2015-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectchromosome mappingen
dcterms.subjectgenetic mapsen
dcterms.subjectmanihot esculenta crantzen
dcterms.subjectdnaen
dcterms.subjectgenesen
dcterms.subjectgenetic markersen
dcterms.subjectpolymorphismen
dcterms.subjectmapas genéticosen
dcterms.subjectadnen
dcterms.subjectmarcadores genéticosen
dcterms.subjectpolimorfismoen
dcterms.typeJournal Article

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