An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies

• Published in: PloS one Vol. 15; no. 5; p. e0232479
• Main Authors: Morales, Karina Y, Singh, Namrata, Perez, Francisco Agosto, Ignacio, John Carlos, Thapa, Ranjita, Arbelaez, Juan D, Tabien, Rodante E, Famoso, Adam, Wang, Diane R, Septiningsih, Endang M, Shi, Yuxin, Kretzschmar, Tobias, McCouch, Susan R, Thomson, Michael J
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 14.05.2020; Public Library of Science (PLoS)
• Subjects: Agricultural economics; Agricultural research; Arrays; Association analysis; Biology and Life Sciences; Breeding; Bumpers, Dale; Chromosomes; Crop science; Density; Deoxyribonucleic acid; DNA; DNA microarrays; Gene mapping; Genes; Genetic aspects; Genetic polymorphisms; Genetic research; Genetics; Genomes; Genomics; Genotyping; Information management; Mapping; Markers; Medicine and Health Sciences; Nucleotides; Oryza sativa; Plant breeding; Plant sciences; Population studies; Quantitative genetics; Quantitative trait loci; Research and Analysis Methods; Rice; Rice farming; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Subpopulations; United States; Louisiana; New York; United States > US; Texas; Philippines
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0232479

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.