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

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 traitspecific 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

A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds

“…The C7AIR includes eight functional SNPs in its design that target important agronomic or physiological traits ( Morales et al, 2020 ). They tag causal variants in genes conferring blast disease resistance ( Pi-ta ; Bryan et al, 2000 ), grain size ( GS3 ; Fan et al, 2006 ; Takano-Kai et al, 2009 ), and eating and cooking quality ( ALK , WAXY ; Okagaki and Wessler, 1988 ; Wang et al, 1995 ; Gao et al, 2003 ).…”

“…Foreground selection was performed in the first three generations using 384 Oligo Pool Assays (OPAs) to establish sets of lines that covered the donor genome ( Thomson et al, 2012 ). Subsequent generations utilized 6 K or 7 K SNP arrays (the C6AIR and C7AIR; Thomson et al, 2017 ; Morales et al, 2020 ), to eliminate non-target introgressions (negative selection) and increase the proportion of recurrent parent background. Length of each donor segment was determined based on the physical position of the marker genotypes.…”

“…As new technology became available, various genotyping methods were employed for MAS during library development. These platforms were SSRs, 384-OPA, the Cornell_6K_Array_Infinium_Rice (C6AIR) and the C7AIR ( McCouch et al, 2002 ; Orjuela et al, 2010 ; Thomson et al, 2012 , 2017 ; Morales et al, 2020 ). Details on each of these genotyping methods are provided in Supplementary Data 1 .…”

“…Details on each of these genotyping methods are provided in Supplementary Data 1 . Genotyping of the final libraries was carried out using the C7AIR SNP array ( Morales et al, 2020 ). The “ACGT” nucleotide file from Genome Studio was exported in the PLINK format and uploaded on TASSEL GUI 2 .…”

Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.)

“…Using the C7AIR, 7098 SNPs were called for N22, Swarna and the DTY-IL [ 58 ]. Frequencies for each SNP across replicated samples were estimated and the most frequent genotype was considered true.…”