Publication Date:
2012-10-08
Description:
Background: Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results: A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs; while AG/GA dimers prevail in transcribed sequences, and accounting for 59.4% of all EST-SSRs. A total of 310 SSRs have been selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have revealed more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferably selected for studies, such as those for genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounting for ~13.5% of the observed phenotypic variation. Conclusion: Di-nucleotide repeats prevail in the apple genome, and AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. The SSR motifs identified in this study serve as valuable resources for pursuing apple genetic studies, and for aiding the apple breeding community.
Electronic ISSN:
1471-2164
Topics:
Biology
Permalink