Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.

Agricultural and Biological Engineering Department University of Florida 1741 Museum Rd Gainesville FL 32611 USA

Centro de Ciencias de la Complejidad Universidad Nacional Autónoma de México Ciudad de México México

Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor New York NY 11724 USA

Departamento de Producción Agrícola y Animal Universidad Autónoma Metropolitana Xochimilco Ciudad de México México

Department of Biochemistry Faculty of Science Palacky University Olomouc Czech Republic

Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA

Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA

Department of Horticulture Washington State University 303c Plant Sciences Building Pullman WA 99164 6414 USA

Federal University of Agriculture Zuru PMB 28 Zuru Kebbi 872101 Nigeria

Institute of Forest Science Madrid Spain

Molecular and Digital Breeding New Cultivar Innovation The New Zealand Institute for Plant and Food Research Limited 120 Mt Albert Road Auckland 1025 New Zealand

National Research Council Canada 110 Gymnasium Pl Saskatoon Saskatchewan S7N 0W9 Canada

Phoenix Bioinformatics 39899 Balentine Drive Suite 200 Newark CA 94560 USA

U S Department of Agriculture Agricultural Research Service NEA Robert W Holley Center for Agriculture and Health Cornell University Ithaca NY 14853 USA

Universidad de la República Uruguay

University of Lagos Nigeria

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