Genome-wide association study (GWAS) is a very powerful method to identify the natural allelic variation present in crop plants causing variation to economically important traits. The recent advances in high throughput genotyping and sequencing technology supplemented greatly to GWAS. Taking this advantage, we selected a total of 382 Chinese cabbage inbred lines for GWAS study. The selected inbred lines are being sequenced using next generation sequencing technology to develop genome wide gene specific single nucleotide polymorphism markers. The morphological and quality traits data were taken from field grown inbred lines. The phenotype and genotype association study will be done with more environmental grown data’s and developed SNP. At the end of this project, gene specific SNP markers will be developed for Chinese cabbage breeding for morphological and quality traits.