Genome-wide association study (GWAS) aims at identifying genetic variants (genotype) that associated with specific traits (phenotype). GWA studies investigates genetic markers cross whole genome of large number of individuals and predicts genotype-phenotype associations by statistical analysis at population level. Whole-genome resequencing can potentially discover all genetic variants. Coupling with phenotypic data, GWAS can be processed to identify phenotype related SNPs, QTLs and candidate genes, which strongly backs up modern animal/plant breeding. SLAF is a self-developed simplified genome sequencing strategy, which discovers genome-wide distributed markers, SNP. These SNPs, as molecular genetic markers, can be processed for association studies with targeted traits. It is a cost-effective strategy in identifying complex traits associated genetic variations.