Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values.

Authors: BRAINARD, SCOTT - University Of Wisconsin; ELLISON, SHELBY - University Of Wisconsin; Simon, Philipp; DAWSON, JULIE - University Of Wisconsin; GOLDMAN, IRWIN - University Of Wisconsin

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2021
Publication Date: 11/15/2021
Citation: Brainard, S., Ellison, S., Simon, P.W., Dawson, J., Goldman, I. 2021. Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values.. Theoretical and Applied Genetics. 135:605–622. https://doi.org/10.1007/s00122-021-03988-8.
DOI: https://doi.org/10.1007/s00122-021-03988-8

Interpretive Summary: The shape of the mature carrot storage root varies from cones or cylinders up to a meter long, to short spheres. Starting in the 1500’s those shapes came to categorize and characterize their ultimate use by the processor or consumer so that all carrot varieties or cultivars today are known by their root shape. While being an essential trait evaluated in all carrot breeding programs, little has been published about the genetics of carrot storage root shape. This study evaluated the shape of 749 carrot cultivars evaluated both visually and with digital image analysis. These cultivars were also genotyped, and using a method known as association analysis, the genetic map locations for several genes were identified for root length, width, curvature of the root shoulder and tip, and the length to diameter ratio. Compelling evidence was provided to support the use of molecular markers for these genes to select for root shape in breeding programs. This study is of interest to carrot growers, seed companies, and researchers studying historical development of familiar crop characteristics.

Technical Abstract: The size and shape of carrot roots are not only major components affecting yield, but are the primary determinants of market class. These quantitative phenotypes have historically been challenging to objectively evaluate, and thus subjective visual assessment of market class remains the primary method by which selection for these traits is performed. However, advancements in digital image analysis have recently made possible the high-throughput quantification of size and shape attributes. Together with a high-quality reference genome, it is now feasible to utilize modern methods of genetic analysis in investigating the genetic control of root morphology. To this end, this study uses both genome wide association analysis and genomic predictions based on genomic-estimated breeding values. This analysis suggests that market class is a highly polygenic trait, under the influence of many small effect QTL, and that relatively large proportions of additive genetic variance for many of the component phenotypes support high predictive ability of genomic-estimated breeding values. This study represents a novel advance in our understanding of the genetic control of market class in carrot root, as well as the possibilities of using genomic predictions for quantitative traits in horticultural crops.