title: Development and utilization of novel intron length polymorphic markers in foxtail millet (Setaria italica (L.) P. Beauv.).
abstract: Introns are noncoding sequences in a gene that are transcribed to precursor mRNA but spliced out during mRNA maturation and are abundant in eukaryotic genomes. The availability of codominant molecular markers and saturated genetic linkage maps have been limited in foxtail millet (Setaria italica (L.) P. Beauv.). Here, we describe the development of 98 novel intron length polymorphic (ILP) markers in foxtail millet using sequence information of the model plant rice. A total of 575 nonredundant expressed sequence tag (EST) sequences were obtained, of which 327 and 248 unique sequences were from dehydration- and salinity-stressed suppression subtractive hybridization libraries, respectively. The BLAST analysis of 98 EST sequences suggests a nearly defined function for about 64% of them, and they were grouped into 11 different functional categories. All 98 ILP primer pairs showed a high level of cross-species amplification in two millets and two nonmillets species ranging from 90% to 100%, with a mean of ∼97%. The mean observed heterozygosity and Nei's average gene diversity 0.016 and 0.171, respectively, established the efficiency of the ILP markers for distinguishing the foxtail millet accessions. Based on 26 ILP markers, a reasonable dendrogram of 45 foxtail millet accessions was constructed, demonstrating the utility of ILP markers in germplasm characterizations and genomic relationships in millets and nonmillets species.
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Sarika
authors.initials: S
authors.lastname: Gupta
authors.forename: Kajal
authors.initials: K
authors.lastname: Kumari
authors.forename: Jyotirmoy
authors.initials: J
authors.lastname: Das
authors.forename: Charu
authors.initials: C
authors.lastname: Lata
authors.forename: Swati
authors.initials: S
authors.lastname: Puranik
authors.forename: Manoj
authors.initials: M
authors.lastname: Prasad
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics*; D016415:Sequence Alignment; D032983:Setaria Plant / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers