Open Access Highly Accessed Research article

Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

Qiong Zhang12, Baiquan Ma12, Hui Li3, Yuansheng Chang3, Yuanyuan Han3, Jing Li1, Guochao Wei12, Shuang Zhao12, Muhammad Awais Khan4, Ying Zhou1, Chao Gu1, Xingzhong Zhang3, Zhenhai Han3, Schuyler S Korban4, Shaohua Li1 and Yuepeng Han1*

  • * Corresponding author: Yuepeng Han

  • † Equal contributors

Author affiliations

1 Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, People’s Republic of China

2 Graduate School of the Chinese Academy of Science, Beijing 100039, People’s Republic of China

3 Institute for Horticultural Plants, China Agricultural University, Beijing 100193, People’s Republic of China

4 Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA

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Citation and License

BMC Genomics 2012, 13:537  doi:10.1186/1471-2164-13-537

Published: 7 October 2012



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.


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 account for 59.4% of all EST-SSRs. A total set of 310 SSRs is 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 detected 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 preferentially selected for studies, such as 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 accounts for ~13.5% of the observed phenotypic variation.


This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae.