Developing genomic databases and integrating the next-generation sequencing tools could advance the efforts of crop improvement and assist in harvesting the actual potential of plant genetic resources. Under changing environmental conditions, exploring the wild and cultivated genetic resources and adjusting their multi-agronomic traits could achieve sustainable solutions for food security challenges. Next-generation sequencing technologies have advanced phenotyping strategies by enabling more accurate assessments under diverse environmental conditions and facilitating the detection of underlying genetic mechanisms. Recently, many omics approaches have been formulated with precise linkage from genome to phenome for biotic and abiotic stress tolerance for the generation of sustainable crop production. Creating crops that support nutritional security requires alternative methods and breeding approaches to diversify the crops at both genetic and phenotypic levels. Here, we demonstrate that integrating the genomics-assisted tools with the 3D chromatin structure of the plant genomes could predict the precise target loci regulating the phenotypic traits of the plants and create an opportunity to improve the crops against the looming challenges of a changing climate and food scarcity. These integrated genomic approaches could assist us in understanding, optimising, and innovating plant breeding strategies under changing climatic conditions.