To meet the challenges and overcome the environmental stressors of agricultural production for an increasing global population, we must understand better how genotype begets phenotype and how the interactions of genotype and the environment influence agriculturally important, complex traits in crops and livestock. Advances in genetics, genomics, engineering, and agricultural, computational, and data sciences can potentially address these challenges. For example, while genome sequencing is now routine even for the large genomes in agriculturally important species, the functional components of these genomes are still largely unknown. Further, engineers have developed new technologies (e.g., robots and sensors) to measure novel biological and environmental variables at high resolution and/or at scale, and data scientists are developing approaches to analyze many types of very large (big data) datasets. Collaboration with agricultural scientists can focus such engineering and big data analytical approaches on analysis of phenotypes and environmental data that will facilitate an understanding of gene function and address fundamental problems of agricultural productivity and sustainability. However, the agricultural genomics and phenomics communities lack a cohesive vision on how to exploit these advances and opportunities, especially where cross-kingdom interactions and interdisciplinary synergies with other fields such as engineering and data science could lead to systems-level solutions [1]. To address this, the US Congress established AG2PI in the 2018 Farm Bill (https://www.congress.gov/bill/115th-congress/house-bill/2).

The crop and livestock research communities (including poultry and aquaculture) have separately begun to address some of these challenges [2,3,4,5]. While the needs of these communities have many commonalities and thus working together holds great potential, there are also significant differences between them. Biology drives some of these differences. For example, plants are sessile, while animals generally are not, and, therefore, plants are hardwired for resistance to some environmental stresses such as drought and heat. Although animals can and do respond to environmental changes, plants exhibit a greater degree of phenotypic plasticity in response to environmental changes, and, as a result, the crop genetics community has focused on accounting for GxE in its predictive models. Nevertheless, GxE is also of importance in livestock, especially when considering the generally high-health conditions in breeding herds compared to commercial production farms.

Differences between crop and livestock research communities are also driven by differences in the associated commercial sectors. For example, a handful of major crop breeding companies provide most of the hybrid corn seed to ~ 80,000 independent US farmers [6]. Traditionally, these companies have not shared information with each other, farmers, or academics. Similar restrictions to data availability apply to swine, poultry, and aquaculture industries, but less so for those concerned with sheep, beef, and dairy cattle. However, academic crop researchers can cost-effectively generate much of their own data. This provides flexibility with respect to experimental design, but financial constraints still often limit the scope of projects [4]. Currently, the ability to generate public genomic/phenomic research data is much more limited in livestock, with some exceptions. For beef and dairy cattle, large databases exist that contain phenotypic trait data from individual animals routinely recorded on production farms; and with certain restrictions, these data are available for research. Combined with the high value of individual animals that contribute significantly to the gene pool and justifies high-density genotyping of such individuals, this has enabled the creation of phenotypic and genomic databases on millions of individuals, offering substantial G2P research opportunities [7]. These collaborations and data sharing even extend across national borders [8].

The crop and livestock research communities are also organized at multiple levels. In both communities, there are many organizations focused on individual species that collectively represent the diversity of species. As well, there are also organizations that represent all crop and livestock commodities (e.g., National Animal Genome Research Program (NAGRP, NRSP-8), American Society of Plant Biology, Crop Science Society of America, and Functional Annotation of Animal Genomes (FAANG)) [9]. Both the crop and livestock research communities have well-established partnerships with industry/commodity groups and individual companies. We suggest that this network of interacting groups, often using similar methods in genetic improvement (see below), could form the basis for an alliance across crop and livestock communities to address G2P. An important AG2PI goal is to identify synergistic opportunities while recognizing the unique needs of each community.

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