Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Abstract

BackgroundFixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.ResultsDesign of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.ConclusionsThe C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.Electronic supplementary materialThe online version of this article (10.1186/s12284-017-0181-2) contains supplementary material, which is available to authorized users.

Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice

“…The 7K array, called the C7AIR, was designed by the McCouch Lab at Cornell University and consists of 7,098 SNPs. The Cornell_7K_Array_Infinium_Rice (C7AIR) design represents an improved version of Cornell_6K_Array_Infinium_Rice (C6AIR) (Thomson et al, 2017). Genotype data used in this study were called using Genome Studio software (Illumina, USA).…”

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

“…Moreover, genome-wide SNP assays have taken the place of conventional gel-based PCR markers, such as SSRs and STSs, in rice breeding programs (McCouch et al 2010). Until recently, genome-wide SNP assays based on several genotyping platforms including Illumina BeadXpress (Chen et al 2011;Thomson et al 2011;Yamamoto et al 2010), Illumina Infinium (Chen et al 2014;Thomson et al 2017;Yu et al 2014), Affymetrix (McCouch et al 2016Singh et al 2015;Zhao et al 2011a), and the KASP marker system (Cheon et al 2018;Pariasca-Tanaka et al 2015;Steele et al 2018;Yang et al 2019) have been developed and applied to rice genetic research and molecular breeding.…”

Transforming Rice Breeding: Re-Designing the Irrigated Breeding Pipeline at the International Rice Research Institute (IRRI)

“…In addition to converting existing trait markers to KASP, we capitalized on the comprehensive existing SNP variation information accumulated from efforts such as the 3000 rice genomes data mining [35] and the Cornell_6K_Array_Infinium_Rice (C6AIR) genotyping [36] of IRRI breeding lines to develop a minimal 10 SNP quality control set with optimized allele frequencies to distinguish any two indica lines by at least one polymorphic SNP. This quality control set found widespread application in parental verification prior to crossing, hybridity verification post crossing, and line variation throughout the breeding and seed production pipelines, minimizing risk of misidentification or carry-over of accidental selfs in crossing and backcrossing schemes.…”