ArticleScientific reports2016
Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 28 citations in OpenAlex.
- Advances in genomic tools for plant breeding: harnessing DNA molecular markers, genomic selection, and genome editing.Biological research · 2024Review
- Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis).Scientific reports · 2022Article
- Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate.Frontiers in plant science · 2022Article
- Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm.Frontiers in plant science · 2022Article
- Review
- Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees.Plants (Basel, Switzerland) · 2021Article
- Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication.Scientific reports · 2017Article
- RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.BMC bioinformatics · 2017Article
- Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches.SpringerPlus · 2016Review
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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