Phenotype identification and genome-wide association study of ear-internode vascular bundles in maize (Zea mays)

The vascular bundle in the ear-internode of maize is a key conduit for transporting photosynthetic materials between "source" and "sink", making it critically important to examine its micro-phenotypes and genetic architecture to identify advantageous characteristics and cultivate high-yielding and high-quality varieties. Unfortunately, the limited observation methods and scope of study precludes any comprehensive and systematic investigations into the microscopic phenotypes and genetic mechanisms of vascular bundle in maize ear-internode. In this study, 47 phenotypic traits were extracted in 495 maize inbred lines using micro computed tomography (Micro-CT) scanning technology and a deep learning-based phenotype acquisition method for stem vascular bundle, which included stem slice-related, epidermis zone-related, periphery zone-related, inner zone-related and vascular bundles-related traits. Phenotypic analysis indicated that there was extensive phenotypic variation of vascular bundle traits in ear-internode, especially that in the inner zone. Of these, 30 phenotypic traits with heritability greater than 0.70 were conducted for GWAS, and a total of 4,225 significant SNPs and 416 candidate genes with detailed functional annotations were identified. Furthermore, 20 genes were highly expressed in stem-related tissues, especially in maize internodes. Functional analysis of candidate genes indicated that the pathways obtained for candidate genes of different trait groups were distinct, mainly involved in vitamin synthesis and metabolism, transport of substances, carbohydrate derivative catabolic process, protein transport and localization, and anatomical structure development. The results of this study will help to further understand the phenotypic traits of stem vascular bundles and provide a reference for revealing the genetic mechanism of maize ear-internode vascular bundles.