High definition 3D models of small legume seed: a close up application to support ancient plant genomics

Abstract

Abstract. Legume seeds are essential for nutrition and play crucial roles in food security, climate change mitigation, biodiversity conservation, and sustainability. Among them, the common bean (Phaseolus vulgaris L.) is the most widely cultivated and vital to the food value chain. Originating in Mesoamerica and independently domesticated there and in the Andes about 8,000 years ago, common beans have adapted to diverse environments globally following the Columbian exchange. Ancient DNA (aDNA) sequencing offers insights into the bean’s adaptation and evolution, but traditional methods struggle with detailed 3D phenotypic analysis due to the beans’ small size and the destructive nature of aDNA extraction. Expensive high-detail optical instruments are not commonly available in genetic labs. This research proposes macro-photogrammetry as a low-cost technique for creating detailed 3D digital replicas of beans. By using samples from archaeological sites in northern Peru, this method preserves phenotypic information despite the destruction of physical samples during DNA extraction. The study details the process of capturing high-detail images with specialized equipment to build a digital phenotype library, preserving the morphological features of ancient beans for further study and future comparison with modern varieties.

Plant phenotyping relevance

マクロ写真測量による小型マメ種子の3D形態取得とデジタル表現型ライブラリ構築が研究の中心であり、植物形態の保存・比較を目的とするため。

Code and data availability

The paper describes macro-photogrammetric 3D models of 26 ancient bean seeds and VR visualization in Sketchfab, but provides no public deposit of the seed images, 3D models, measurement data, or analysis code. The only URLs given are the article DOI, a PRIN grant shortlink, and the INCREASE project website, none of a 3

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