ArticleFrontiers in plant science2022
Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice.
Article in Frontiers in plant science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 29 citations in OpenAlex.
- Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.Journal of applied genetics · 2026Article
- Research progress on genomic selection breeding technology for crops.Protoplasma · 2026Review
- MianxinNo.1: a modern cultivar genome-informed SNP array based on cGPS technology for genomics-assisted breeding in cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Development and application of a genotyping by target sequencing single-nucleotide polymorphism array panel in Salix suchowensis.BMC genomics · 2026Article
- A new genetic architecture for PHS resistance in rice: deciphering the epistatic interactions of three major QTL.Frontiers in plant science · 2026Article
- Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).BMC plant biology · 2025Article
- Integrative genomic and transcriptomic dissection of salt tolerance forFrontiers in plant science · 2025Article
- Comprehensive Morphological and Molecular Insights into Drought Tolerance Variation at Germination Stage inPlants (Basel, Switzerland) · 2024Article
- Analysis of quantitative trait loci and candidate gene exploration associated with cold tolerance in rice (Frontiers in plant science · 2024Article
- Review
- Genomic landscape of theFrontiers in plant science · 2023Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rice is a globally cultivated crop and is primarily a staple food source for more than half of the world's population. Various single-nucleotide polymorphism (SNP) arrays have been developed and utilized as standard genotyping methods for rice breeding research. Considering the importance of SNP arrays with more inclusive genetic information for GWAS and genomic selection, we integrated SNPs from eight different data resources: resequencing data from the Korean World Rice Collection (KRICE) of 475 accessions, 3,000 rice genome project (3 K-RGP) data, 700 K high-density rice array, Affymetrix 44 K SNP array, QTARO, Reactome, and plastid and GMO information. The collected SNPs were filtered and selected based on the breeder's interest, covering all key traits or research areas to develop an integrated array system representing inclusive genomic polymorphisms. A total of 581,006 high-quality SNPs were synthesized with an average distance of 200 bp between adjacent SNPs, generating a 580 K Axiom Rice Genotyping Chip (580 K _ KNU chip). Further validation of this array on 4,720 genotypes revealed robust and highly efficient genotyping. This has also been demonstrated in genome-wide association studies (GWAS) and genomic selection (GS) of three traits: clum length, heading date, and panicle length. Several SNPs significantly associated with cut-off, -log
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