title: A high density consensus map of rye (Secale cereale L.) based on DArT markers.
abstract: BACKGROUND
  Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers.
  
  
  RESULTS
  Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers.
  
  
  CONCLUSIONS
  Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization.
authors.affiliation: Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, Poland.
authors.forename: Paweł
authors.initials: P
authors.lastname: Milczarski
authors.forename: Hanna
authors.initials: H
authors.lastname: Bolibok-Brągoszewska
authors.forename: Beata
authors.initials: B
authors.lastname: Myśków
authors.forename: Stefan
authors.initials: S
authors.lastname: Stojałowski
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Heller-Uszyńska
authors.forename: Magdalena
authors.initials: M
authors.lastname: Góralska
authors.forename: Piotr
authors.initials: P
authors.lastname: Brągoszewski
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Uszyński
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.forename: Monika
authors.initials: M
authors.lastname: Rakoczy-Trojanowska
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics*; D018745:Genome, Plant; D005838:Genotype; D008957:Models, Genetic; D016133:Polymerase Chain Reaction / Q000379:methods; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D012434:Secale / Q000235:genetics*
chemical_list: D005819:Genetic Markers