An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.)

Authors: TURNER, SARAH - University Of Wisconsin; Ellison, Shelby; Senalik, Douglas; Simon, Philipp; SPALDING, EDGAR - University Of Wisconsin; MILLER, NATHAN - University Of Wisconsin

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2018
Publication Date: 11/27/2018
Citation: Turner, S.D., Ellison, S.L., Senalik, D.A., Simon, P.W., Spalding, E.P., Miller, N.D. 2018. An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.). Frontiers in Plant Science. 9(1703):1-17. https://doi.org/10.3389/fpls.2018.01703.
DOI: https://doi.org/10.3389/fpls.2018.01703

Interpretive Summary: In comparing among diverse varieties of cultivated carrot, there is a wide range of variation in the shape and size of carrot roots and shoots. Root size is important to farmers as a measure of productivity of the crop, and carrot shoot, or top, size varies widely, with large-topped varieties being more competitive with weeds. The shape of carrot roots is important to carrot growers and consumers because root shape varies widely among different varieties. While variation in carrot root and shoot morphology is important, accurate measurements of morphology are time consuming and challenging to capture. In this study we evaluated several aspects of carrot root and shoot size and shape both with traditional hand measurements, and with computer analysis of digital images of the same carrot plants. The image analytical system was successfully developed for this study, and it required only about one-third the time it took to gather the same, or more information, as hand measurements. The correlations between measures taken with both methods were very high, indicating that they both measured the same aspects of the plants. The image analysis system was also used to evaluate morphological variation in a carrot population that varied for root and shoot shape and size, and 40 genes were identified to control much of that variation. This image analysis system is of interest for growers and seed companies working with all vegetable crops, and with many fruit, agronomic, and ornamental crops. The research results are also of interest to these same stakeholders, as well as to researchers studying the fundamental bases of plant growth and development.

Technical Abstract: Carrot is a globally important crop, yet methods to rapidly and reliably capture quantitative measurements for agronomic characteristics are lacking. Phenotypes of interest include straightforward measurements, such as plant height and root length, in addition to more complex traits such as shoot architecture, which is important for successful crop establishment, and root shape, which is the primary delimiter for variety classification. To address this bottleneck, we present a high-throughput, automated image analysis platform to extract traits of practical importance for carrot breeding and genetics. The utility of this method to reliably capture phenotypic variation is validated by the observation of high correlations between manual and algorithm-derived measurements for 917 individual plants. Additionally, this approach enables the capture of shape information for carrot shoots and roots, allowing evaluation of traits which are not readily measured by hand. We further demonstrate the potential of this pipeline in relation to meaningful objectives in carrot breeding and genetics: assessment of repeatability in a six-parent diallel mating design and detection of quantitative trait loci (QTL) in an F2 mapping population with 316 individuals. We find high levels of repeatability within growing environment, with low to moderate repeatability across environments. Interestingly, we also observe co-localization of QTL for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. Given existing time and labor restrictions, the development of a high-throughput image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies by increasing the number of individuals and phenotypes that can be reliably evaluated.