ArticlePloS one2020
An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies.
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37 citing papers in PubMed, 1 synthesis or guideline pooled it, 100 citations in OpenAlex.
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- A multi-race blast resistance locus identified and validated in US elite rice via association and biparental mapping.The plant genome · 2026Article
- ConvCGP: A convolutional neural network to predict genetic values of agronomic traits from compressed genome-wide polymorphisms.The plant genome · 2026Article
- Multi-environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool.The plant genome · 2026Article
- Genome-wide association mapping, phylogenetic study, and multivariate analysis of component traits of grain yield in wheat under heat stress conditions.Plant molecular biology · 2026Article
- Development of a cost-effective high-throughput mid-density 5K genotyping assay for germplasm characterization and breeding in groundnut.The plant genome · 2025Article
- Divergent genetic architecture of cold stress tolerance inFrontiers in plant science · 2025Article
- The Ratio of ARice (New York, N.Y.) · 2024Article
- Identification and analysis of low light responsive yield enhancing QTLs in rice.Scientific reports · 2024Article
- Developing an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions.BMC genomics · 2024Article
- Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis.The plant genome · 2024Article
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- Development of KASP markers, SNP fingerprinting and population genetic analysis ofFrontiers in plant science · 2024Article
- Genomic prediction and QTL analysis for grain Zn content and yield inJournal of plant biochemistry and biotechnology · 2024Article
- Impact of Seed Origin and Genetic Drift of Improved Rice Variety IR841 in Benin.Rice (New York, N.Y.) · 2023Article
- A multiplexed plant-animal SNP array for selective breeding and species conservation applications.G3 (Bethesda, Md.) · 2023Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- Article
- DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis.International journal of molecular sciences · 2023Article
- 3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes.Plant methods · 2023Article
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14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.
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