**7.4 Challenges**

The genetic resources collections, which are held collectively in various gene banks, harbour a wealth of undisclosed allelic variants. Now the challenge is how to efficiently identify and exploit the useful variation of these collections to exploit in crop improvement. The challenges stand as stampling block to make use of these collections are (1) selection of genotypes, (2) handling genomic resources, (3) demarcation of promoter region, (4) characterization of regulatory region, and (5) higher sequencing costs. The selection of germplasm to be 'mined' is one of the utmost challenges face the scholars because of the huge genetic resources collections. To overcome the aforementioned challenges, we must (1) narrow down the core collection to a manageable size while maintaining the variability, (2) refine phenotyping protocols to increase the efficiency of allele mining, (3) exploit the developments in allele mining, association genetics and comparative genomics by combining expertise from several disciplines, including molecular genetics, statistics and bioinformatics, (4) develop cheaper and faster sequencing platforms for high through put detection of allelic variations (5) develop flexible computational tools to manage genetic resources, select desirable alleles, analyze the functional nucleotide diversity to predict specific nucleotide changes responsible for altered function, accurately predict the core promoter region based on the representation/over-representation of consensus regulatory motifs, and get the snapshot of the regulatory elements which can be further examined through suitable experiments.
