Phenomics: unlocking the hidden genetic variation for breaking the barriers in yield and stress tolerance

Abstract

The rate of genetic gain in yield, quality, input use efficiency and adaptability of crops to biotic and abiotic stresses must be improved significantly to achieve global food and nutritional security by 2050. To achieve this goal, deciphering the physiological genetic basis and assembly of component traits through analytical breeding is necessary. The two pillars of analytical breeding are genotyping and phenotyping. Advances in genotyping technologies such as single-nucleotide polymorphism genotyping and genotyping by sequencing have made deep genotyping cheaper and quicker, while phenotyping has lagged behind and thus remains a rate limiting step. Recently, phenomics has emerged as a new way of accurately phenotyping large set of genotypes. Phenomics employ non-invasive sensors and advanced computational platforms for non-destructive and high-throughput phenotyping. The depth of component phenotypic traits and the spatio-temporal dynamic phenotypic data generated in phenomics are enormous and unparallel to the conventional phenotyping. The utility of phenomics in QTL mapping and genome-wide association studies has already been demonstrated in important food crops. Phenomics has high potential for phenome-wide association studies, genomics selection models for enhancing selection efficiency, and genetic-ecophysiological crop simulation models for prediction of genotype-phenotypes relationship, in silico phenotyping and ideotype design. With the advancement in the depth of phenome data acquisition and analyses capabilities of phenomics, phenome assisted breeding and phenomic selection is anticipated to be a reality in near future. Complementary use of conventional phenotyping and advanced phenomics is suggested to assist in fundamental discoveries and analytical crop breeding.