Integrating 3D imaging, GWAS, and single-cell transcriptome approaches to elucidate root system architecture in...

Area of Science:

• Plant genetics
• Molecular biology
• Tree physiology

Background:

• Root system architecture (RSA) is crucial for tree nutrient uptake and stability.
• Genetic factors controlling RSA are not well understood.
• Simon poplar (Populus simonii) is an important tree species for studying wood properties.

Purpose of the Study:

• To investigate the genetic architecture and regulatory networks of RSA in Simon poplar.
• To identify key genes and molecular mechanisms controlling root development.
• To develop advanced methods for quantifying RSA traits.

Main Methods:

• Genome-wide association study (GWAS) on 303 P. simonii accessions.
• Multiomics analyses including transcriptome and single-cell RNA-seq (scRNA-seq).
• Genetic transformation and molecular assays in poplar (Populus alba × Populus glandulosa).
• Automated 3D spatial imaging for RSA trait quantification.

Main Results:

• GWAS identified S-phase kinase-associated protein 2B (PsiSKP2B) as a candidate gene associated with 6 RSA traits.
• PsiSKP2B was identified as a key regulator in meristematic tissue cells, crucial for lateral root (LR) development.
• Overexpression of PsiSKP2B in 84k poplar lines increased LR number and density by 65.9% and 98.6%, respectively.
• PsiSKP2B modulates LR development via interaction with PsiWOX4 or PsiZHD9 in atrichoblast cells.

Conclusions:

• PsiSKP2B is a critical genetic determinant of RSA in Simon poplar.
• A novel atrichoblast-dependent regulatory mechanism involving PsiSKP2B governs LR development.
• The study provides a comprehensive multiomics framework and advanced imaging techniques for RSA research in trees.