title: Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.
abstract: We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17-79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9-21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, "Oryza ISM-ILP marker" database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Badoni
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Sweta
authors.initials: S
authors.lastname: Das
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
authors.forename: Yogesh K
authors.initials: YK
authors.lastname: Sayal
authors.affiliation: Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.
authors.forename: S
authors.initials: S
authors.lastname: Gopalakrishnan
authors.affiliation: Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.
authors.forename: Ashok K
authors.initials: AK
authors.lastname: Singh
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
authors.forename: Atmakuri R
authors.initials: AR
authors.lastname: Rao
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Pinky
authors.initials: P
authors.lastname: Agarwal
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
mesh_terms: D030541:Databases, Genetic; D004587:Electrophoresis, Agar Gel / Q000379:methods; D020869:Gene Expression Profiling; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D057166:High-Throughput Screening Assays; D054643:INDEL Mutation; D020407:Internet; D007438:Introns; D009929:Organ Size; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D012639:Seeds
chemical_list: D005819:Genetic Markers