Adapting crops to future harsher conditions of a major concern for food security.

Agrigenomics is a potential method to improve the adaptability of crops through increasing agrobiodiversity.

It is expected that wild relatives represent an important reservoir of adaptations to extreme environmental stresses.

NGS can be used to identify wild relatives carrying adaptations that can be used for improvement of crop adaptation in breeding programs. It can also be used to identify genes and polymorphisms associated with adaptations for targeted improvement.

Next-generation sequencing promotes the development and commercialization of bioproducts which affect applied fields like biocontrol, stress protection, and arable land.

For example, the microorganisms that potentially play a role in crop health and disease suppression can be identified with a culture-dependent approach using a next-generation sequencing-based platform and powerful bioinformatics analysis.

NGS may impact (i) the detection of new bio-resources for biocontrol and plant growth promotion; (ii) the optimization of formulation; (iii) risk assessment studies for bio-products; and (iv) stabilization of the biocontrol effect under field conditions.

Advances in NGS and phenotyping platforms have accelerated the genomics-assisted breeding.

Genomics is consistently increasing the diversity of alleles available for animal breeding.

Genomic information can accelerate breeding programs by selecting a combination of genomic markers associated with desirable traits. And genome-wide arrays are used to predict the future health and performance of the newborn animals.

Microorganisms colonized in the gut of livestock can be sequenced and analyzed to enable optimization of animal feed and diagnosis of infections.

Antimicrobial resistance (AMR) is a major cause of morbidity and mortality in humans and animals on a global scale.

NGS is a promising method to understand and prepare for emerging AMR threats.

To be specific, sequencing such as whole genome sequencing can be used to comprehensively monitor AMR epidemiology through exploring the rise and spread of resistant pathogenic strains and lineages.

The sequencing-based platform also allows researchers to track the evolutionary origins of antimicrobial resistance microbes and determine the corresponding therapies.