Abstract
Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.
Highlights
Carrot is a globally important crop that originated in Central Asia (Vavilov, 1992; Iorizzo et al, 2013) with a secondary center of diversity in Asia Minor (Banga, 1957)
Samples included individual plants from two sources: a diallel mating design with six diverse inbred parents and an F2 population that segregates for plant height, shoot biomass, and storage root shape
Of the 124 images that failed, two were missing hand measurements, eight had root defects such as sprangle, 60 had poor lighting or shadowing, eight overlapped with the edge of the image or the black line separating the shoot and root, and 46 failed for reasons which were not readily identifiable, with possible explanations including the presence of numerous fibrous roots, interference of labels, and/or diminutive plant size
Summary
Carrot is a globally important crop that originated in Central Asia (Vavilov, 1992; Iorizzo et al, 2013) with a secondary center of diversity in Asia Minor (Banga, 1957). Selective breeding has since improved taproot size, shape, and uniformity, resulting in forms that have served as the primary delimiter of variety classification since the 1600s (Simon et al, 2008). A primary breeding objective is to achieve rapidly growing, sturdy shoots without compromising the size and shape of the storage root. Methods to measure both shoots and roots more objectively are required (Horgan, 2001). These methods should be quantitative and objective, replacing traditional subjective descriptors such as circular, obovate, obtriangular, and narrow oblong to describe global root shape, or blunt, slightly pointed, and strongly pointed to describe the distal end (or tip) of the storage root. Methods should characterize shoot architecture more comprehensively than typical measurements of plant height, width, and biomass
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