title: Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple.
abstract: 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 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, People's Republic of China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Zhang
authors.forename: Baiquan
authors.initials: B
authors.lastname: Ma
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Yuansheng
authors.initials: Y
authors.lastname: Chang
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Han
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Guochao
authors.initials: G
authors.lastname: Wei
authors.forename: Shuang
authors.initials: S
authors.lastname: Zhao
authors.forename: Muhammad Awais
authors.initials: MA
authors.lastname: Khan
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhou
authors.forename: Chao
authors.initials: C
authors.lastname: Gu
authors.forename: Xingzhong
authors.initials: X
authors.lastname: Zhang
authors.forename: Zhenhai
authors.initials: Z
authors.lastname: Han
authors.forename: Schuyler S
authors.initials: SS
authors.lastname: Korban
authors.forename: Shaohua
authors.initials: S
authors.lastname: Li
authors.forename: Yuepeng
authors.initials: Y
authors.lastname: Han
mesh_terms: D002874:Chromosome Mapping; D018900:Dinucleotide Repeats / Q000235:genetics; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D008293:Malates / Q000378:metabolism*; D027845:Malus / Q000235:genetics* / Q000378:metabolism; D018895:Microsatellite Repeats; D040641:Quantitative Trait Loci
chemical_list: D008293:Malates; C030298:malic acid