title: Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].
abstract: The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (∼48%) was prevalent when compared with dinucleotide repeats (∼46%). Of the 28 342 microsatellites, 21 294 (∼75%) primer pairs were successfully designed, and a total of 15 573 markers were physically mapped on 9 chromosomes of foxtail millet. About 159 markers were validated successfully in 8 accessions of Setaria sp. with ∼67% polymorphic potential. The high percentage (89.3%) of cross-genera transferability across millet and non-millet species with higher transferability percentage in bioenergy grasses (∼79%, Switchgrass and ∼93%, Pearl millet) signifies their importance in studying the bioenergy grasses. In silico comparative mapping of 15 573 foxtail millet microsatellite markers against the mapping data of sorghum (16.9%), maize (14.5%) and rice (6.4%) indicated syntenic relationships among the chromosomes of foxtail millet and target species. The results, thus, demonstrate the immense applicability of developed microsatellite markers in germplasm characterization, phylogenetics, construction of genetic linkage map for gene/quantitative trait loci discovery, comparative mapping in foxtail millet, including other millets and bioenergy grass species.
authors: National Institute of Plant Genome Research NIPGR, Aruna Asaf Ali Marg, New Delhi 110 067, India.
authors: Garima
authors: G
authors: Pandey
authors: Gopal
authors: G
authors: Misra
authors: Kajal
authors: K
authors: Kumari
authors: Sarika
authors: S
authors: Gupta
authors: Swarup Kumar
authors: SK
authors: Parida
authors: Debasis
authors: D
authors: Chattopadhyay
authors: Manoj
authors: M
authors: Prasad
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D018895:Microsatellite Repeats; D031782:Pennisetum / Q000235:genetics; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D032983:Setaria Plant / Q000145:classification / Q000235:genetics*; D018911:Trinucleotide Repeats
chemical_list: D005819:Genetic Markers
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