A System for Dosage-Based Functional Genomics in Poplar.

Area of Science:

• Plant genomics
• Functional genomics
• Quantitative genetics

Background:

• Gene dosage, or copy number variation, is crucial for understanding gene regulation, quantitative traits, and heterosis.
• Investigating gene dosage is challenging in sexually reproducing species, but clonal propagation in elite poplar (Populus spp.) offers a unique avenue.
• Interspecific hybridization and clonal propagation are key to developing elite poplar varieties, with altered gene dosage potentially driving hybrid performance.

Purpose of the Study:

• To establish a genome-wide structural variation system for dosage-based functional genomics and breeding in poplar.
• To create a resource for investigating the role of gene dosage in poplar quantitative traits and heterosis.

Main Methods:

• Pollination of Populus deltoides with gamma-irradiated Populus nigra pollen to generate F1 seedlings.
• Induction of dosage lesions, specifically deletions and insertions of chromosomal segments (indel mutations), in the F1 progeny.
• High-precision dosage analysis to detect and characterize indel mutations across the genome.

Main Results:

• Generation of over 500 F1 seedlings with dosage lesions.
• Detection of indel mutations in approximately 55% of the progeny.
• Indels cumulatively tiled over 99% of the genome, with an average of 10 indels per gene, exhibiting variation in length, position, and number per individual.

Conclusions:

• The developed system provides a powerful tool for dosage-based functional genomics and breeding in poplar.
• The resulting F1 population is a valuable resource for future studies on phenotype and transcriptome data, elucidating the contribution of gene dosage to quantitative traits and heterosis.
• This approach overcomes limitations in studying gene dosage in sexually reproducing species by leveraging poplar's clonal propagation capabilities.