Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression...

Area of Science:

• Plant Genetics
• Molecular Biology
• Agronomy

Background:

• Heterosis, or hybrid vigor, in rice is crucial for crop yield but is often affected by environmental conditions and genetic interactions.
• Hybrid weakness, a phenomenon where hybrids perform worse than their parents, is a significant challenge in rice breeding.
• Understanding the molecular basis of hybrid weakness is essential for developing more robust rice hybrids.

Purpose of the Study:

• To investigate the transcriptomic changes associated with hybrid weakness in rice.
• To determine the relationship between non-additive gene expression (NAE), allele-specific gene expression (ASE), and hybrid weakness.
• To explore the potential role of environmental factors in influencing these molecular mechanisms.

Main Methods:

• Generated nine rice hybrids using a 3x3 incomplete diallel cross design.
• Conducted field experiments to evaluate grain yield and identify hybrids exhibiting mid-parent heterosis (MPH) or mid-parent hybrid weakness (MPHW).
• Performed transcriptome sequencing on panicles during the seed-filling stage for MPH and MPHW hybrids.

Main Results:

• Four out of nine hybrids displayed MPHW, while five showed MPH for grain yield.
• Transcriptome analysis revealed significantly higher proportions of ASE genes (22.65%-45.97%), often with mono-allele expression, in MPHW hybrids compared to MPH hybrids (4.80%-5.69%).
• An independence test showed a significant correlation between enhanced NAE and ASE in MPHW hybrids.

Conclusions:

• Hybrid weakness in rice is strongly associated with enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) at the transcriptome level.
• The findings suggest that unfavorable environmental conditions may trigger hybrid weakness by upregulating ASE and NAE.
• This research provides molecular insights into hybrid weakness, potentially guiding future breeding strategies for improved rice hybrids.