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Background  Fixed 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.    Results  Design 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.    Conclusions  The 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 material  The online version of this article (10.1186/s12284-017-0181-2) contains supplementary material, which is available to authorized users.

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