Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple
文献类型：期刊论文
| 作者 | Zhao,Shuang3,4; Zhang,Qiong3,4; Ma,Baiquan3,4; Li,Hui2; Chang,Yuansheng2; Han,Yuanyuan2; Li,Jing3; Wei,Guochao3,4; Khan,Muhammad Awais1; Zhou,Ying3 |
| 刊名 | BMC Genomics
 |
| 出版日期 | 2012-10-07 |
| 卷号 | 13期号:1 |
| ISSN号 | 1471-2164 |
| DOI | 10.1186/1471-2164-13-537 |
| 英文摘要 | AbstractBackgroundApple 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. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/1471-2164-13-537 |
| 出版者 | BioMed Central |
| 源URL | [http://202.127.146.157/handle/2RYDP1HH/723]  |
| 专题 | 中国科学院武汉植物园 |
| 通讯作者 | Han,Yuepeng |
| 作者单位 | 1.University of Illinois; Department of Natural Resources and Environmental Sciences 2.China Agricultural University; Institute for Horticultural Plants 3.the Chinese Academy of Sciences; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden 4.Graduate School of the Chinese Academy of Science |
| 推荐引用方式 GB/T 7714 | Zhao,Shuang,Zhang,Qiong,Ma,Baiquan,et al. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple[J]. BMC Genomics,2012,13(1). |
| APA | Zhao,Shuang.,Zhang,Qiong.,Ma,Baiquan.,Li,Hui.,Chang,Yuansheng.,...&Han,Yuepeng.(2012).Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple.BMC Genomics,13(1). |
| MLA | Zhao,Shuang,et al."Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple".BMC Genomics 13.1(2012). |
入库方式： OAI收割
来源：武汉植物园
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