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Development and utilization of novel SSR s in foxtail millet [ S etaria italica (L.) P. Beauv.]
Author(s) -
Gupta Sarika,
Kumari Kajal,
Muthamilarasan Mehanathan,
Subramanian Alagesan,
Prasad Manoj
Publication year - 2013
Publication title -
plant breeding
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.583
H-Index - 71
eISSN - 1439-0523
pISSN - 0179-9541
DOI - 10.1111/pbr.12070
Subject(s) - biology , microsatellite , foxtail , genetics , primer (cosmetics) , genotyping , genetic marker , triticeae , population , setaria , molecular breeding , allele , genotype , botany , gene , genome , demography , organic chemistry , chemistry , sociology
Although the foxtail millet [ S etaria italica (L.) P. Beauv.] is recently regarded as a model crop for studying functional genomics of biofuel grasses, its genetic improvement to some extent was limited due to the non‐availability of molecular markers, particularly the microsatellite markers and the saturated genetic linkage map. Considering this, we attempted to generate a significant number of microsatellite markers in cultivar ‘Prasad’. Two hundred and fifty‐six clones were sequenced to generate 41.82‐kb high‐quality sequences retrieved from genomic library enriched with dinucleotide repeat motifs. Microsatellites were identified in 194 (76%) of the 256 positive clones, and 64 primer pairs (pp) were successfully designed from 95 (49%) unique SSR ‐containing clones. The 67.4% primer designing ability, 100% PCR amplification efficiency and 45.3% polymorphic potential in the parents of F 2 mapping population established the efficacy of genomic microsatellites. All the 64 microsatellite markers displayed high level of cross‐species amplification (~67%) in 10 millets and non‐millets species. These experimental findings suggest the utility and efficacy of SSR s in diverse genotyping applications, resolving QTL s, phylogenetic relationships and transferability in several important grass species.