Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.

Area of Science:

• Genomics
• Plant Biology
• Transcriptomics

Background:

• Gene expression variation is crucial for phenotypic diversity, especially in species with complex genomes.
• Pan-transcriptome construction is vital, but its regulatory mechanisms and functional impacts remain understudied.

Purpose of the Study:

• To systematically investigate the regulation and functional consequences of pan-transcriptome variation in maize.
• To associate transcriptomic variations with phenomic variations using genome-wide association studies (GWAS).
• To identify novel sequences absent in the reference genome and assess their contribution to maize traits and heterosis.

Main Methods:

• Analysis of RNA-sequencing data from 368 diverse maize inbred lines.
• Identification of genes with expression presence and absence variation (ePAV).
• Genome-wide association studies (GWAS) using ePAV for agronomic and metabolic traits.
• Modified assembly strategy to discover novel sequences and genomic PCR validation.
• Simulation analysis and development of test-cross populations to study gene contribution to heterosis.

Main Results:

• Nearly one-third of nuclear genes exhibit expression presence and absence variation (ePAV), often playing regulatory roles and influenced by distant eQTLs.
• GWAS identified associations between ePAV and 15 agronomic phenotypes and 526 metabolic traits.
• 2,355 novel sequences (1.9 Mb total) were discovered, absent in the reference genome, with two NBS-LRR candidates linked to disease resistance and flavonoids.
• Dispensable genes contribute to heterosis, and the maize kernel pan-transcriptome may approach 63,000 genes.

Conclusions:

• Expression presence and absence variation (ePAV) is a significant source of genetic variation in maize, linking transcriptomics to phenomics.
• Novel sequences and dispensable genes contribute to important agronomic traits, including heterosis.
• This study provides valuable resources and perspectives for understanding maize kernel regulation and improving crop breeding.