Isolating phyllotactic patterns embedded in the secondary growth of sweet cherry ( Prunus avium L.) using magnetic resonance imaging.

Abstract

Background Epicormic branches arise from dormant buds patterned during the growth of previous years. Dormant epicormic buds remain just below the surface of trees, pushed outward from the pith during secondary growth, but maintain vascular connections. Epicormic buds can be activated to elongate into a new shoot, either through natural processes or horticultural intervention, to potentially rejuvenate orchards and restructure tree architecture. Because epicormic structures are embedded within secondary growth, tomographic approaches are a useful method to study them and understand their development. Results We apply techniques from image processing to determine the locations of epicormic vascular traces embedded within secondary growth of sweet cherry ( Prunus avium L.), revealing the juvenile phyllotactic pattern in the trunk of an adult tree. Techniques include the flood fill algorithm to find the pith of the tree, edge detection to approximate the radius, and a conversion to polar coordinates to threshold and segment phyllotactic features. Intensity values from magnetic resonance imaging (MRI) of the trunk are projected onto the surface of a perfect cylinder to find the locations of traces in the "boundary image". Mathematical phyllotaxy provides a means to capture the patterns in the boundary image by modeling phyllotactic parameters. Our cherry tree specimen has the conspicuous parastichy pair (2,3), phyllotactic fraction 2/5, and divergence angle of approximately 143°. Conclusions The methods described provide a framework not only for studying phyllotaxy, but also for processing of volumetric image data in plants. Our results have practical implications for orchard rejuvenation and directed approaches to influence tree architecture. The study of epicormic structures, which are hidden within secondary growth, using tomographic methods also opens the possibility of studying genetic and environmental influences such structures.

Plant phenotyping relevance

MRI画像と画像処理を組み合わせ、樹幹内部の維管束痕と葉序パターンを抽出・定量する方法が研究の中心であり、植物形態のフェノタイピング手法に該当する。

Code and data availability

The paper's availability statement explicitly provides authors' analysis code on GitHub and the raw MRI data on figshare, both paper-specific and publicly actionable.