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Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice
- Source :
- Scientific Reports
- Publication Year :
- 2016
- Publisher :
- Nature Publishing Group, 2016.
-
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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Genetic Markers
Genetic Linkage
Population
Quantitative Trait Loci
Quantitative trait locus
Oryza
Genes, Plant
01 natural sciences
Genome
Genetic analysis
Article
03 medical and health sciences
INDEL Mutation
Genetic linkage
Genetic variation
Databases, Genetic
education
Phylogeny
Genetics
Electrophoresis, Agar Gel
education.field_of_study
Internet
Multidisciplinary
Polymorphism, Genetic
biology
Gene Expression Profiling
food and beverages
Genetic Variation
Organ Size
biology.organism_classification
Introns
High-Throughput Screening Assays
030104 developmental biology
Genetic marker
Seeds
Genome, Plant
010606 plant biology & botany
Subjects
Details
- Language :
- English
- ISSN :
- 20452322
- Database :
- OpenAIRE
- Journal :
- Scientific Reports
- Accession number :
- edsair.doi.dedup.....3e79d7893112a94a18013b274bbeab6a
- Full Text :
- https://doi.org/10.1038/srep23765