Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice

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, −log10p-value >7.0, were detected in GWAS, and the GS predictabilities for the three traits were more than 0.5, in both rrBLUP and convolutional neural network (CNN) models. The Axiom 580 K Genotyping array will provide a cost-effective genotyping platform and accelerate rice GWAS and GS studies.

A computational model for sample dependence in hypothesis testing of genomic data

“…We use two resources of rice genomic data sets: 44K_SNP data 11 and 580K_KNU data 12 . Both data sets consist of SNP genotype and phenotype information of rice accessions.…”

Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security

“…Helps in rapid breeding for a particular trait [95] Marker-assisted selection Pyramided genes of high grain weight, stripe rust, and leaf rust resistance [96] Rice QTL mapping Heat tolerance [97] QTL mapping Pre-harvest sprouting resistance [98] SNP genotyping array RiceSNP50 Functional genomics and molecular breeding [99] 580 K SNP array Genomic selection and GWAS [100] Genotyping-by-sequencing Pre-breeding and improvement [101] Genomic prediction Rice improvement [102] GWAS Adaptability to dry direct-seeded rice (DDSR) system [103] Rice pangenome genotyping array (RPGA) SNP genotyping Genetic improvement [104] QTL-seq using NIL-F 2 Grain length and weight [103] SNP-based QTL mapping Panicle traits [104] Table 2. Cont.…”

Application of SNP Markers to Identify Genetic Variation on Mutant Lines of Adan-Krayan, Special Local Rice from North Kalimantan

“…Morales et al [10] reported that an SNP array containing 7,098 markers had been developed from the Cornell-IR LD Rice Array (C7AIR). In addition, Rice3K56 containing 56,606 SNP markers [11] and 580K SNP array [12] had also been developed. SNP markers for selecting essential traits in rice are also starting to be assembled [13], [14], [15].…”