title: A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes.
abstract: 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.
authors.affiliation: Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. jcsotos@unal.edu.co.
authors.forename: Johana Carolina
authors.initials: JC
authors.lastname: Soto
authors.affiliation: Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. jortizqu@uwyo.edu.|Present address Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. jortizqu@uwyo.edu.
authors.forename: Juan Felipe
authors.initials: JF
authors.lastname: Ortiz
authors.affiliation: Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia. lauraperlaza@gmail.com.|Present address Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany. lauraperlaza@gmail.com.
authors.forename: Laura
authors.initials: L
authors.lastname: Perlaza-Jiménez
authors.affiliation: Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. axvasquezc@unal.edu.co.
authors.forename: Andrea Ximena
authors.initials: AX
authors.lastname: Vásquez
authors.affiliation: International Center for Tropical Agriculture (CIAT), Cali, Colombia. L.A.Becerra@cgiar.org.
authors.forename: Luis Augusto Becerra
authors.initials: LA
authors.lastname: Lopez-Lavalle
authors.affiliation: INRES-Plant Breeding University of Bonn, Bonn, Germany. boby.mathew@hotmail.com.
authors.forename: Boby
authors.initials: B
authors.lastname: Mathew
authors.affiliation: INRES-Plant Breeding University of Bonn, Bonn, Germany. j.leon@uni-bonn.de.
authors.forename: Jens
authors.initials: J
authors.lastname: Léon
authors.affiliation: Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia. abernal@uniandes.edu.co.
authors.forename: Adriana Jimena
authors.initials: AJ
authors.lastname: Bernal
authors.affiliation: INRES-Plant Breeding University of Bonn, Bonn, Germany. ballvora@uni-bonn.de.
authors.forename: Agim
authors.initials: A
authors.lastname: Ballvora
authors.affiliation: Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. celopezc@unal.edu.co.
authors.forename: Camilo Ernesto
authors.initials: CE
authors.lastname: López
mesh_terms: D002874:Chromosome Mapping; D016000:Cluster Analysis; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D002365:Manihot / Q000235:genetics*; D057865:Plant Immunity / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins