title: Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes.
abstract: A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of 1/72 bp, 1 in 58 bp in non-coding sequences, increasing to 1/47 bp upon the addition of the remaining genotypes. Within analysed DNA fragments, alleles at different SNP positions displayed linkage disequilibrium indicative of haplotype structures. On average 2.7 haplotypes were found in sugar beet lines, and haplotype conservation in expressed genes appeared to exceed 500 bp in length. Seven different genotyping techniques including SNP detection by MALDI-TOF mass spectrometry, pyrosequencing and fluorescence scanning of labelled nucleotides were employed to perform 712 segregation analyses for 538 markers in three F(2) populations. Functions were predicted for 492 mapped sequences. Genetic maps comprised 305 loci covering 599.8 cM in population K1, 241 loci distributed over 636.6 cM in population D2, and 166 loci over 507.1 cM in population K2, respectively. Based on 156 markers common to more than one population an integrated map was constructed with 524 loci covering 664.3 cM. For 377 loci the genome positions of the most similar sequences from A. thaliana were identified, but little evidence for previously presented ancestral genome structures was found.
authors.affiliation: Department of Plant Breeding and Yield Physiology, Max-Planck-Institute for Plant Breeding Research , Carl-von-Linné Weg 10, 50827 Cologne, Germany. katharina.schneider@gsf.de
authors.forename: Katharina
authors.initials: K
authors.lastname: Schneider
authors.forename: Dagmar
authors.initials: D
authors.lastname: Kulosa
authors.forename: Thomas Rosleff
authors.initials: TR
authors.lastname: Soerensen
authors.forename: Silke
authors.initials: S
authors.lastname: Möhring
authors.forename: Martin
authors.initials: M
authors.lastname: Heine
authors.forename: Gregor
authors.initials: G
authors.lastname: Durstewitz
authors.forename: Andreas
authors.initials: A
authors.lastname: Polley
authors.forename: Eberhard
authors.initials: E
authors.lastname: Weber
authors.lastname: Jamsari
authors.forename: Jens
authors.initials: J
authors.lastname: Lein
authors.forename: Uwe
authors.initials: U
authors.lastname: Hohmann
authors.forename: Emma
authors.initials: E
authors.lastname: Tahiro
authors.forename: Bernd
authors.initials: B
authors.lastname: Weisshaar
authors.forename: Britta
authors.initials: B
authors.lastname: Schulz
authors.forename: Georg
authors.initials: G
authors.lastname: Koch
authors.forename: Christian
authors.initials: C
authors.lastname: Jung
authors.forename: Martin
authors.initials: M
authors.lastname: Ganal
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D027461:Beta vulgaris / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics*; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers; D018745:Genome, Plant; D006239:Haplotypes; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers