title: A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions.
abstract: The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg erecta (Col-0×Ler-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and Ler-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/Ler-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used Arabidopsis accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.
authors.affiliation: Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden. Daniel.Pacurar@plantphys.umu.se
authors.forename: Daniel Ioan
authors.initials: DI
authors.lastname: Păcurar
authors.forename: Monica Lăcrămioara
authors.initials: ML
authors.lastname: Păcurar
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Street
authors.forename: John Desmond
authors.initials: JD
authors.lastname: Bussell
authors.forename: Tiberia Ioana
authors.initials: TI
authors.lastname: Pop
authors.forename: Laurent
authors.initials: L
authors.lastname: Gutierrez
authors.forename: Catherine
authors.initials: C
authors.lastname: Bellini
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D002874:Chromosome Mapping; D003001:Cloning, Molecular; D005819:Genetic Markers; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment
chemical_list: D029681:Arabidopsis Proteins; D005819:Genetic Markers