title: Assessment of genetic diversity in Zingiberaceae through nucleotide binding site-based motif-directed profiling.
abstract: Functional motif-directed profiling was performed with 15 nucleotide binding site (NBS) primer-enzyme combinations to identify and elucidate the phylogenetic relationships among 15 genotypes of the family Zingiberaceae. We retrieved 167 polymorphic bands (24.85 %), with an average of 11.13 bands per primer. Mean polymorphism rates were detected using MseI (26 %), RsaI (21 %), and AluI (28 %) as restriction enzymes. The polymorphism information content (PIC) for each NBS primer-enzyme combination ranged from 0.48 to 0.76 with a mean value of 0.65. The 38 NBS profiling markers had PIC values ranging from 0.3 to 0.6 and exhibited good power to discriminate between genotypes. Comparison of NBS profiling with microsatellite data for the same set of genotypes exhibited a correlation value of 0.78, P ≤ 0.001. Our study suggests that genetic variability assessment could be more efficient if it targeted genes that exhibit functionally relevant variation, rather than random markers.
authors.affiliation: Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar 751003, India. rajkumar.joshi@yahoo.co.in
authors.forename: Raj Kumar
authors.initials: RK
authors.lastname: Joshi
authors.forename: Sujata
authors.initials: S
authors.lastname: Mohanty
authors.forename: Basudeba
authors.initials: B
authors.lastname: Kar
authors.forename: Sanghamitra
authors.initials: S
authors.lastname: Nayak
mesh_terms: D001665:Binding Sites; D005819:Genetic Markers / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D059372:Nucleotide Motifs; D009711:Nucleotides / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics*; D030521:Zingiberaceae / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D009711:Nucleotides