Plant phenotypic traits refer to physical, physiological, and biochemical traits that can reflect a plant cell, its tissue, organs, population structure, and functional characteristics. Fruit stones and carbonized seeds are the most prevalent plant remains discovered in ancient archeological research sites. Size and shape are the two primary quantifiable features that can be used to investigate the evolution of plant phenotypic traits. This research analyzes the prevailing methods used domestically and internationally that measure phenotypic features of seeds and fruit stones. This analysis develops as follows: During the initial phase, a traditional and user-friendly morphological measurement method concentrates on calculating the straightforward linear separation between anatomical points and the size of the stone or seed being analyzed. The measurement index undergoes a shift from the straightforward determination of individual variables to the intricate determination of many variables, succeeded by a thorough examination of multivariate data, with gradual enhancement of the comprehensiveness of the index. In phase two, the Geometric Morphometrics method, which focuses on shape, combines automatic image recognition, intelligent measurement software, and a variety of data statistical analysis methods to distinguish size and shape data based on the geometric spatial relationship between anatomical points and outlines. The two-dimensional data are transformed into a high precision and high resolution three-dimensional geometric shape parameter reconstruction of plant phenotypes. Micro-CT and other technologies can not only measure the external morphology and reconstruct the volume, but also observe the internal structure and measure more characteristics. As a result, the quantitative reconstruction and result visualization of the geometric spatial network of points, lines, and planes are clearer and more accurate. In the next step, the significance and application of crop seeds/fruit stones phenotypic traits measurement is introduced systematically. This involves the identification of plant species, differentiation of wild/cultivated species, process of crop domestication, spread, and diversification, agricultural planting structure, production, and processing, as well as cultural behavior, function of an archaeological site, and social hierarchy. Subsequently, problems that still exist in the research are then proposed, such as (1) C-14 year dating is necessary; (2) the measurement index measurements will be affected by the intact of the charred plant remains; (3) immature seeds/fruit stones will affect the results of measurement and analysis. Criteria for distinguishing between mature and immature, immature and wild species may not yet be established, e.g., too low a sample size may result in large errors and affect the statistical analysis results of seeds/fruit stones. Finally, this research proposes prospects for future studies on plant phenotypes, which include: (1) Use of improved measurement samples: desiccated or waterlogged seed/stone samples are ideal for study because they are almost completely undeformed. The extremely arid area of Xinjiang is an important direction for phenotypic measurement in the future; (2) implementation of innovative measurement methods: three-dimensional scanning should be applied to improve the scanning accuracy and reduce scanning errors. While ensuring measurement accuracy, the sample measurement speed is accelerated to carry out high throughput measurement and reduce the complexity of post-processing, such as three-dimensional point cloud data processing and image segmentation; (3) establishment and sharing of database of phenotypic trait measurement results to more fully explore the causes of changes in crop seeds/fruit stones phenotypic trait. This paper is the first systematic introduction and comprehensive review of the morphological measurement of crop seeds/fruit stones remains, whose proposed research direction stands as one of the key topics in the research frontier of plant remains, offering extensive potential future prospects in application and development.
