Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1.
We developed 74 microsatellite marker primer pairs yielding 76 polymorphic loci, specific for the short arm of rye chromosome 1R (1RS) in wheat background. Four libraries enriched for microsatellite motifs AG, AAG, AC and AAC were constructed from DNA of flow-sorted 1RS chromosomes and 1,290 clones were sequenced. Additionally, 2,778 BAC-end-sequences from a 1RS specific BAC library were used for microsatellite screening and marker development. From 724 designed primer pairs, 119 produced 1RS specific bands and 74 of them showed polymorphism in a set of ten rye genotypes. We show that this high attrition rate was due to the highly repetitive nature of the rye genome consisting of a large number of transposable elements. We mapped the 76 polymorphic loci physically into three regions (bins) on 1RS; 29, 30 and 17 loci were assigned to the distal, intercalary and proximal regions of the 1RS arm, respectively. The average polymorphism information content increases with distance from the centromere, which could be due to an increased recombination rate along the chromosome arm toward's the telomere. Additionally, we demonstrate, using the data of the whole rice genome, that the intra-genomic length variation of microsatellites correlates (r = 0.87) with microsatellite polymorphism. Based on these results we suggest that an analysis of the microsatellite length variation is conducted for each species prior to microsatellite development, provided that sufficient sequence information is available. This will allow to selectively design microsatellite markers for motifs likely to yield a high level of polymorphism.
Kofler
Robert
R
Department for Agrobiotechnology, Institute for Plant Production Biotechnology, University of Natural Resources and Applied Life Sciences, Konrad Lorenz Str. 20, 3430 Tulln, Austria. tamas.lelley@boku.ac.at
Bartos
Jan
J
Gong
Li
L
Stift
Gertraud
G
Suchánková
Pavla
P
Simková
Hana
H
Berenyi
Maria
M
Burg
Kornel
K
Dolezel
Jaroslav
J
Lelley
Tamas
T
D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D030561:Databases, Nucleic Acid; D002523:Edible Grain / Q000235:genetics; D018895:Microsatellite Repeats; D011110:Polymorphism, Genetic; D012434:Secale / Q000235:genetics*; D013045:Species Specificity; D014908:Triticum / Q000235:genetics
D017931:DNA Primers; D018744:DNA, Plant