eQTL Analysis Elucidates the Genetic Basis Underlying Transgressive Gene Expression in Nelumbo Hybrids

Area of Science:

• Genetics
• Molecular Biology
• Evolutionary Biology

Background:

• Hybridization can lead to novel gene expression patterns, influencing hybrid vigor or dysfunction.
• The specific roles of cis- and trans-regulatory variants in hybrid expression novelty are not well understood.

Purpose of the Study:

• To investigate the genetic architecture of transgressive gene expression in interspecific hybrids.
• To identify cis- and trans-regulatory variants influencing expression novelty.

Main Methods:

• Expression quantitative trait locus (eQTL) mapping was performed on a multi-generational Nelumbo population (parental species, F1 hybrids, backcrossed F2 individuals).
• Matrix eQTL analysis under an additive linear model was utilized to identify SNP-gene associations.

Main Results:

• Over 147,000 cis-eQTLs and 151,000 trans-eQTLs were identified, regulating thousands of cis- and trans-eGenes.
• Trans-eQTLs demonstrated stronger regulatory effects than cis-eQTLs and were enriched for transcription factors.
• Transgressive expression was more prevalent in segregating backcrossed individuals, linked to regulatory variants in key metabolic pathways like benzylisoquinoline alkaloid biosynthesis.

Conclusions:

• Trans-regulatory rewiring is a predominant driver of transgressive gene expression in hybrid populations.
• The study provides genetic resources for understanding regulatory network contributions to transcriptional variation and phenotypes in interspecific hybrids.