As important genetic resources and powerful tool, high density single nucleotide polymorphsim (SNP) arrays are indispensable for genomic analysis of complex traits. We developed a high-density wheat SNP array which was named as wheat660k and comprised 630,517 variants based on 51M SNP variants. Based on the genotyping data in another large panel, we updated the SNP array and finished a new version of wheat genotyping SNP array named as wheat660-v2. From the above SNP set we developed a 55K wheat breeding array. Several specialities occurred for wheat660-v2 array. 1) There were 660,009 SNP sites in one array, so it owned a feature of high density and high efficiency. 2) Most of SNPs were subgenome specific markers in wheat. 3) The cost of this array was low because of many orders especially in China. 4) Several applications occurred for these two arrays such as population structure analysis, genetic map construction, QTL mapping analysis, gene fine mapping and genome selection breeding and so on. One case of application was construction of a highdensity genetic map. For a RIL population derived from Xiaoyan54×Jing411, the number of polymorphic markers between the parental lines was 190,878. The number of polymorphic markers for this population, which could be used for map construction, was 137,631. Another example used 55K array in which a RIL population derived from a common wheat and a synthetic wheat was used. The ratio of polymorphic markers between the parental lines was about 50%.

The third application example was used in breeding program and study of wheat wild relatives in the reference published by Shenghui Zhou (Plant Biotechnol J.c2018 Mar;16(3):818-827. doi: 10.1111/pbi.12831). Using the wheat 660K-v2 array to genotype a segregating Agropyron F1 population derived from an interspecific cross between two cross-pollinated diploid collections 'Z1842' [A. cristatum (L.) Beauv.] (male parent) and 'Z2098' [A. mongolicum Keng] (female parent). Genetic linkage maps were constructed using 913 SNP markers distributed among seven linkage groups spanning 839.7 cM. Using wheat660k-v2, we also fine mapped or cloned important genes in wheat using a method combining linkage analysis and GWAS.

In conclusion, the high density Affymetrix Axiom genotyping array wheat660-v2 was developed. Based on 660K SNP array, we finished a 55K breeding array. And the 660k high density genotyping array and the 55k breeding array were widely used in China now.