Abstract
Due mainly to large genome size and prevalence of repetitive sequences in the nuclear genome of spruce (Picea Mill.), it is very difficult to develop single-copy genomic microsatellite markers. We have developed and characterized 25 polymorphic, single-copy genic microsatellites from white spruce (Picea glauca (Moench) Voss) EST sequences and determined their informativeness in white spruce and black spruce (Picea mariana (Mill.) B.S.P.) and inheritance in black spruce. White spruce EST sequences from NCBI dbEST were searched for the presence of microsatellite repeats. Forty-seven sequences containing dinucleotide, trinucleotide, tetranucleotide and compound repeats were selected to develop primers. Twenty-five of the designed primer pairs yielded scorable amplicons, with single-locus patterns, and were characterized in 20 individuals each of white spruce and black spruce. All 25 microsatellites were polymorphic in white spruce and 24 in black spruce. The number of alleles at a locus ranged from two to 18, with a mean of 8.8 in white spruce, and from one to 17, with a mean of 7.6 in black spruce. The expected heterozygosity/polymorphic information content ranged from 0.10 to 0.92, with a mean of 0.67 in white spruce, and from 0 to 0.93, with a mean of 0.59 in black spruce. Microsatellites with dinucleotide and compound repeats were more informative than those with trinucleotide and tetranucleotide repeats. Eighteen microsatellite markers polymorphic between the parents of a black spruce controlled cross inherited in a single-locus Mendelian fashion. The microsatellite markers developed can be applied for various genetics, genomics, breeding, and conservation studies and applications.
Highlights
Microsatellites or simple sequence repeats (SSR) are co-dominant, highly polymorphic and reproducible molecular genetic markers, which have been widely used for various biological, breeding, forensics and conservation studies and applications
We have developed and characterized 25 polymorphic, single-copy genic microsatellites from white spruce ( Picea glauca ) Expressed Sequenced Tags (ESTs) sequences and determined their informativeness in white spruce and black spruce ( Picea mariana ) and inheritance in black spruce
White spruce EST sequences from NCBI dbEST were searched for the presence of microsatellite repeats
Summary
Microsatellites or simple sequence repeats (SSR) are co-dominant, highly polymorphic and reproducible molecular genetic markers, which have been widely used for various biological, breeding, forensics and conservation studies and applications. Expressed sequence tag (EST) sequences in the NCBI database and transcriptome sequences provide an important resource for identifying microsatellite sequences and developing cDNA-based genic microsatellite markers in plants [e.g., 2,3], including conifer trees Due mainly to large genome size and prevalence of repetitive sequences in the nuclear genome of spruce ( Picea ), it is very difficult to develop single-copy genomic microsatellite markers. We have developed and characterized 25 polymorphic, single-copy genic microsatellites from white spruce ( Picea glauca ) EST sequences and determined their informativeness in white spruce and black spruce ( Picea mariana ) and inheritance in black spruce
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