Integrating dynamic high-throughput phenotyping and genetic analysis to monitor growth variation in foxtail millet

Foxtail millet [Setaria italica (L.) Beauv] is a C₄ graminoid crop cultivated mainly in the arid and semiarid regions of China for more than 7000 years. Its grain highly nutritious and is rich in starch, protein, essential vitamins such as carotenoids, folate, and minerals. To expand the utilisation of foxtail millet, efficient and precise methods for dynamic phenotyping of its growth stages are needed. Traditional foxtail millet monitoring methods have high labour costs and are inefficient and inaccurate, impeding the precise evaluation of foxtail millet genotypic variation.

This study introduces a high-throughput imaging system (HIS) with advanced image processing techniques to enhance monitoring efficiency and data quality. The HIS can accurately extract a range of key growth feature parameters, such as plant height (PH), convex hull area (CHA), side projected area (SPA) and colour distribution, from foxtail millet images. Compared with traditional manual measurements, this HIS improved data quality and phenotyping of the key foxtail millet growth traits. High-throughput phenotyping combined with a genome-wide association study (GWAS) revealed genetic loci associated with dynamic growth traits, particularly plant height (PH), in foxtail millet. The loci were linked to genes involved in the gibberellic acid (GA) synthesis pathway related to PH.

The HIS developed in this study enables the efficient and dynamic monitoring of foxtail millet phenotypic traits. It significantly improves the quality of data obtained for phenotyping key growth traits. The integration of high-throughput phenotyping with GWAS provides new insights into the genetic underpinnings of dynamic growth traits, particularly plant height, by identifying associated genetic loci in the GA synthesis pathway. This methodological advancement opens new avenues for the precise phenotyping and exploration of genetic resources in foxtail millet, potentially enhancing its utilisation.