Insights into the maize pan-genome and pan-transcriptome.

Area of Science:

• Genomics
• Plant Biology
• Maize Genetics

Background:

• Species genomes are dynamic, comprising core genes (in all individuals) and dispensable genes (in subsets), collectively forming the pan-genome.
• Understanding the pan-genome is crucial for characterizing genetic diversity and evolutionary potential within a species.

Purpose of the Study:

• To characterize the maize (Zea mays) pan-genome using transcriptome sequencing.
• To investigate the extent of genetic variation within the maize germplasm base.
• To identify genetic loci associated with key developmental transitions.

Main Methods:

• Transcriptome sequencing of seedling RNA from 503 maize inbred lines.
• Identification and clustering of representative transcript assemblies (RTAs).
• Linkage disequilibrium mapping and genome-wide association studies (GWAS).

Main Results:

• Identified 8681 RTAs, with only 16.4% expressed in all lines and 82.7% in subsets.
• 76.7% of RTAs with single nucleotide polymorphisms (SNPs) mapped to unique genetic positions.
• GWAS revealed loci associated with juvenile-to-adult vegetative and vegetative-to-reproductive transitions.

Conclusions:

• The maize genome, within the studied germplasm, appears restricted, suggesting limited new gene discovery from further sampling.
• A significant portion of maize genetic variation exists outside the reference genome.
• Pan-genome analysis provides insights into traits critical for plant fitness and adaptation.