69 The Bigger Picture of Phenomics: Whole-System Support for Systems Research, Models and Databases

Abstract

Abstract Phenomics started with Mendel’s elegantly simple empirical studies. Soon after, Fisher discovered purines were rich in nuclei of all cells. A century later, we have the technology to compare the actual base pair sequence of DNA and RNA with the outward expressions of phenotypes. We have sire evaluation based on genomic and phenomic measure. But, being human, it is quite common to get immersed in exciting technology and tend to forget why we developed the technology in the first place. We only refer to ensuring a stable efficient food supply of plants and animals in the reports that we expect decision makers to read and give us more money. It is, however, truly wonderful that we now have the techniques to study the questions of the ages. But the future of phenomics is built on the foundations of the past. In 1974, A. E. Freeman and others convened a meeting under the mechanism of the newly formed Regional Research Project 2 on Defining the Inefficiency of Animal Production. From that workshop came the first modern multistate genetic study in dairy cattle with the objective to compare the phenotypes (milk component production, energy and nitrogen metabolism, hormones) of dairy animals that were born from bulls of High (+795 kg PTAM) and Low (167 kg PTAM) bulls. Please remember this study was designed in the mid 1970s and the first data collected in the early 1980s, decades before efficient methods of DNA and RNA composition were available. Studies conducted at Washington State University demonstrated marked genetic and environmental differences in adipose tissues of dairy animals. Enzymes involved with catabolic reactions were highly associated with High PTAM bulls while enzymes associated with anabolic reactions in adipose tissue were more closely related to increased energy intake regardless of genetic background. With mRNA chips, we were able, after almost 40 years, to directly relate variation in mRNA expression in the adipose tissue with the genetic background of the animals. This was the first such discovery in the field, and has led to more defined and expansive phenomics studies. In the year 2023, the use of genomics, phenomics, databases, large scale, cooperative studies and team science are specific recommendations, strategies and goals of the USDA, NIFA, The National Academies, and Land-Grant Universities. The AgBioData consortium is one example of international teams working together to expand the use of genetic and genomic databases, to prepare undergraduate and graduate level educational materials on FAIR databases and to encourage and support sustainable, robustly funded public and private partnerships in the use of integrated studies and large databases, including phenomics, with the sole purpose of expanding a robust, resilient, safe and plentiful food supply.