Plant Science Innovation, Center for



Sunil K. Kenchanmane Raju

Addie M. Thompson

James C. Schnable

Date of this Version



Kenchanmane Raju, S. K., A. M. Thompson, and J. C. Schnable. 2020. Advances in plant phenomics: From data and algorithms to biological insights. Applications in Plant Sciences 8(8): e11386. doi:10.1002/aps3.11386


This is an open access article under the terms of the Creative Commons Attribution License.


The measurement of the characteristics of living organisms is referred to as phenotyping (Singh et al., 2016). While the use of phenotyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genetics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent of inexpensive genotyping tools, crop functional genomics has entered the “big data” era, but efficient large-scale phenotyping is still an impediment hindering plant functional genomics. The precise measurement of plant traits both throughout the growth cycle and across environments is expensive and labor intensive. A convergence of interdisciplinary efforts has led to the development of new technologies for nondestructive phenotyping in plants to measure large numbers of traits accurately with higher throughput (Close and Last, 2011). Improvements in imaging and automation, as well as in data processing and analytics, are helping to fill significant gaps in efforts to employ these new technologies to connect genetic variation with phenotypes (Yang et al., 2020). In recent years, plant phenomics research has transitioned from the development of methods and molecular genetic analysis of model plants in controlled environments toward accelerated efforts for applications in plant breeding, association studies, and stress phenotyping in crops grown under complex field conditions (Costa et al., 2018). In this special issue, “Advances in Plant Phenomics: From Data and Algorithms to Biological Insights,” we present six papers that capture plant phenomics extending to multiple scales, from field-wide traits, to individual plots or plants, to specific gene interactions.