Increased grain production, fiber development and/or plant biomass through controlling plant development is one of the major goals of crop breeding programs. Until recently, progress in breeding programs had largely been due to empirical observations by farmers and botanists, with limited insights into the underlying physiological mechanisms. Understanding the mechanisms underlying the phenotypic variability resulting from breeding techniques such as grafting, will certainly contribute to increased yields. Next generation sequencing technologies are providing new tools for the study of developmental biology of crop plants. By identifying the genes and other regulatory elements controlling important traits such as pollen development, fertility, and seed vigor, NGS is uncovering markers for selection and improvement in breeding programs.

Plants respond to numerous stresses faced during their growth cycle, and development of plant tolerance to abiotic and biotic stress is another major goal of selection and breeding programs.  Advanced genomic and transcriptomic tools such as microarrays and NGS have revealed miRNAs play a critical role in almost all biological and metabolic processes, and provide a unique strategy for plant improvement.  miRNAs regulatory roles makes them key targets for genetic manipulations to engineer abiotic stress tolerance in crop plants.