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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-10-07

AUTHORS

Qiong Zhang, Baiquan Ma, Hui Li, Yuansheng Chang, Yuanyuan Han, Jing Li, Guochao Wei, Shuang Zhao, Muhammad Awais Khan, Ying Zhou, Chao Gu, Xingzhong Zhang, Zhenhai Han, Schuyler S Korban, Shaohua Li, Yuepeng Han

ABSTRACT

BackgroundApple 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.ResultsA 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.ConclusionsThis 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. More... »

PAGES

537

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    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-13-537

    DOI

    http://dx.doi.org/10.1186/1471-2164-13-537

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1024678092

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23039990


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