As the third-generation molecular marker, SNP plays an important role in many aspects of molecular breeding. SNP testing for species with existing catalog chip can be conducted directly. However, if the species studied by researchers do not have a catalog SNP chip, or the SNP loci of the catalog chip cannot effectively represent the information of the specific species or traits concerned by researchers, it is necessary to customize the SNP chip first. Through SNP typing, on the one hand, QTL mapping, GWAS, selection signal analysis and other strategies can be adopted to find SNP marker site related to traits for molecular marker assisted breeding; on the other hand, genome selection method is adopted for molecular breeding at genome wide level.