PAG-VI: MICROSATELLITE MARKERS TARGETING GENES IN LOBLOLLY PINE
Plant & Animal Genome VI Conference
Town & Country Hotel, San Diego, CA, January 18-22, 1998.
P65
MICROSATELLITE MARKERS TARGETING GENES IN LOBLOLLY PINE
CHRISTINE G. ELSIK, Virginia L. Minihan, Sarah E. Hall, Claire G. Williams
Texas A&M University, Genetics and Forest Science, Mail Stop 2135, College Station, TX 77843-2135
Loblolly pine is characterized by a large complex genome with 22 pg DNA per haploid nucleus and 76% repetitive DNA. The high proportion of repetitive DNA makes the movement from genetic to physical mapping very difficult. Markers in close proximity to genes may make chromosome landing possible in large genomes. We have isolated microsatellites in close proximity to genes using a filter hybrid capture technique. Three loblolly pine genomic libraries were enriched for microsatellite motifs:
(CCT)n, (CGT)n, (GCT)n, (GGT)n;
(AGT)n, (CTT)n, (GAT)n, (GTT)n;
(CGTT)n, (CTGT)n, (AGGT)n, (GAGT)n, (GGAT)n.
Sequences flanking microsatellites were compared to nucleotide and amino acid sequence databases using Basic Local Alignment Search Tool (BLAST), with a probability of 0.05 as the cutoff value for significant high scoring segment pairs (HSPs). BLASTX searched for significant HSPs between translated nucleotide query sequences in all six reading frames and amino acid sequences in public protein databases. BLASTN compared query nucleotide sequences to nucleotides sequences in public databases; only matches within Pinaceae were considered positive using BLASTN. Microsatellites were removed from query sequences before executing the BLAST search. Sequences with a minimum of 100 nucleotides of non-microsatellite sequence were used in the search. BLASTX indicated that 45 of 88 sequences searched (51%) matched other eukaryotic amino acid sequences. BLASTN indicated that 3 of 88 sequences searched matched pine nucleotide sequences. The 47 positive matches included 18 matches to plant amino acid and/or nucleotide sequences. These sequences offer unique insights into microsatellite function in the loblolly pine genome.
Plant & Animal Genome VI Conference