Wheat (Triticum aestivum L.) is an important staple cereal crop of Western-Himalayan region of India. The production and productivity of wheat in Western Himalayas of Jammu and Kashmir is affected by several biotic and abiotic stresses. Therefore, we have evaluated a set of >5000 wheat genotypes for cold/freezing tolerance, stripe rust, foliar blight, cereal leaf beetle, army worm and pre-harvest sprouting tolerance. The trait evaluation of this huge germplasm set has led to the identification of very important and new sources of cold tolerance, disease resistance and insect resistance. The candidate genotypes thus identified will prove useful in future wheat breeding programs. The analysis of trait dat also helped to develop mini-core sets of 300-400 genotypes. The mini-core set is being evaluated for several important bio-chemicals induced in response to cold, disease and insect resistance. Efforts are also being made to conduct metabolite profiling using few candidate genotypes for each trait. Genotyping data is also being generated for this huge collection of germplasm for the study of marker-trait associations (MTAs) through GWAS. The GWAS is expected to provide set of tools including QTLs, genes, markers for their use in wheat molecular breeding programs.