Homoeologous exchanges contribute to branch angle variations in rapeseed: Insights from transcriptome, QTL-seq and...

Area of Science:

• Plant genetics and breeding
• Molecular biology
• Agricultural science

Background:

• Branch angle (BA) is a key trait affecting crop yield and planting density.
• Understanding the genetic regulation of BA in rapeseed (Brassica napus) is crucial for crop improvement.
• Current knowledge on BA regulatory mechanisms in rapeseed is limited.

Purpose of the Study:

• To elucidate the molecular mechanisms controlling branch angle in rapeseed.
• To identify genetic factors and genomic regions associated with variations in branch angle.
• To investigate the role of homoeologous exchanges and specific genes in BA regulation.

Main Methods:

• Transcriptome sequencing of 37 rapeseed accessions with diverse BA phenotypes.
• Co-expression network analysis to identify gene modules correlated with BA.
• QTL-seq analysis to pinpoint genomic regions associated with BA.
• Gene expression analysis, including overexpression and gene editing (RNAi, CRISPR) of candidate genes.

Main Results:

• Abaxial branch segments showed higher auxin levels and lower expression of TCP1 and GA20ox3 compared to adaxial segments.
• Two gene modules significantly correlated with BA were identified, containing known BA-related genes.
• Specific homoeologous exchanges (HEs) at telomeric regions of chromosomes A09, A02-C02, and A07-C06 were associated with large and small BA phenotypes, respectively.
• BnaA07.WRKY40.b was identified as a candidate gene, with its overexpression increasing BA and gene editing reducing it.

Conclusions:

• Homoeologous exchanges play a significant role in shaping rapeseed plant architecture and branch angle.
• WRKY40 homologues, specifically BnaA07.WRKY40.b, are novel regulators of branch angle in rapeseed.
• The findings provide insights into the genetic basis of plant architecture and offer potential targets for rapeseed breeding programs aiming to optimize yield.