title: Direct haplotype-specific DNA sequencing.
abstract: Determining haplotype-specific DNA sequence information is very important in a wide range of research fields. However, no simple and robust approaches are currently available for determining haplotype-specific sequence information. We have addressed this problem by developing a very simple and robust haplotype-specific sequencing approach. We utilise the fact that DNA sequencing polymerases are sensitive to 3'end mismatches in the sequencing primer. By using two sequencing primers with 3'end corresponding to the two alleles in a given SNP locus, we are able to obtain allele-specific DNA sequences from both alleles. We evaluated this direct haplotype-specific approach by determining haplotypes within the intron 2 sequence of the fructan-6-fructosyltransferase (6-ft) gene in Lolium perenne L. We obtained reliable haplotype-specific sequences for all primers and genotypes evaluated. We conclude that the haplotype-specific sequencing is robust, and that the approach has a potentially very wide application range for any diploid organism.
authors.affiliation: Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Norway.
authors.forename: Heidi
authors.initials: H
authors.lastname: Rudi
authors.forename: Knut-Erik
authors.initials: KE
authors.lastname: Gylder
authors.forename: Odd
authors.initials: O
authors.lastname: Arne Rognli
authors.forename: Knut
authors.initials: K
authors.lastname: Rudi
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000032:analysis* / Q000235:genetics*; D006239:Haplotypes; D008969:Molecular Sequence Data; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004247:DNA