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Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential

文献类型： 外文期刊

作者： Biswas, Manosh Kumar 1 ; Liu, Yuxuan 4 ; Li, Chunyu 1 ; Sheng, Ou 1 ; Mayer, Christoph 5 ; Yi, Ganjun 1 ;

作者机构： 1.Guangdong Acad Agr Sci, Inst Fruit Tree Res, Guangzhou, Guangdong, Peoples R China

2.Minist Agr, Key Lab South Subtrop Fruit Biol & Genet Resource, Guangzhou, Guangdong, Peoples R China

3.South China Agr Univ, Coll Life Sci, Guangzhou, Guangdong, Peoples R China

4.Huazhong Agr Univ, Minist Educ, Key Lab Hort Plant Biol, Wuhan, Hubei, Peoples R China

5.Forschungsmuseum Alexander Koenig, D-53113 Bonn, Germany

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2015 年 10 卷 6 期

页码：

收录情况： SCI

摘要： The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.

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