Kazakhstan is a major wheat exporter in the region. However, an average wheat grain yield has not changed since 1960’s in the country and plant breeding is mainly based on conventional ways of selection. Here, we developed the first segregating population for Kazakhstan with the cross of UK and KZ wheats. Thus, the crossing of two wheat varieties adapted and breed for diverse climatic conditions allows one to discovery the exotic allelic variations present in certain environment. As such, many adaptation and yield related QTL were discovered among of which two plant height related QTL with large additive effects (which we have not seen before) were used to develop NILs for each locus. The double NILs possessing both loci simultaneously, were also generated. These points made it interesting to ask how the single and combined height increasing QTL perform and interact respectively in an isogenic background. A large field experiments on NILs in KZ made it possible to dissect height and yield components. As the NIL effect was true, both QTL regions were fine-mapped using map-based approach and height related genes within the mapped interval were pulled out. Here, the fully sequenced exons and whole genomes of NIL parents were useful for target marker development. Besides, we established a large Central-Asian wheat panel. The panel was genetically fingerprinted and analysed. The haplotype lead approache in this population helped us to further squeeze the mapped interval. Moreover, this new resource and its genomic data will allow the local wheat breeders to maximise the genetic diversity in the parental selection and to fully utilise the genetic diversity which something has not been captured so far using only conventional breeding technologies.