title: Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential.
abstract: 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.
authors.affiliation: Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China; The College of Life Science, South China Agricultural University, Guangzhou, China.
authors.forename: Manosh Kumar
authors.initials: MK
authors.lastname: Biswas
authors.affiliation: Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Yuxuan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China.
authors.forename: Chunyu
authors.initials: C
authors.lastname: Li
authors.affiliation: Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China.
authors.forename: Ou
authors.initials: O
authors.lastname: Sheng
authors.affiliation: Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Mayer
authors.affiliation: Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China.
authors.forename: Ganjun
authors.initials: G
authors.lastname: Yi
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification; D005819:Genetic Markers; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D028521:Musa / Q000235:genetics*; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D005819:Genetic Markers; D035683:MicroRNAs