Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development

Area of Science:

• Plant Molecular Biology
• Genetics and Genomics
• Cotton Fiber Development

Background:

• Natural antisense transcripts (NATs) are prevalent in eukaryotes but their regulatory roles in plant gene expression, especially in fiber development, remain underexplored.
• Understanding NATs' function is crucial for elucidating complex gene regulatory networks in economically important crops like cotton.

Purpose of the Study:

• To investigate the function of small RNAs derived from NATs in regulating cotton fiber cell development.
• To identify and characterize genes involved in fuzz fiber development using map-based cloning in tetraploid cotton.

Main Methods:

• Map-based cloning was employed to identify the naked seed mutant gene (N1) in tetraploid cotton.
• Histochemical staining assays were used to analyze the promoter activity and NAT production.
• Deep sequencing of small RNAs was performed to identify small interfering RNAs (siRNAs) generated from bidirectional transcription.

Main Results:

• A novel gene, GhMML3_A12, encoding a MYBMIXTA-like transcription factor, was cloned and associated with fuzz fiber development.
• Extremely low expression of GhMML3_A12 in the naked seed mutant (N1) correlated with NAT production driven by its 3' antisense promoter.
• Bidirectional transcription of GhMML3_A12 generated double-stranded RNAs, producing 21-22 nt small RNAs that mediate mRNA self-cleavage, leading to naked seeds and inhibited lint fiber.

Conclusions:

• This study reports the first instance of gene-mediated NATs and siRNAs directly controlling fiber development in cotton.
• The findings reveal a novel regulatory pathway involving NATs and siRNAs in cotton fiber production, impacting seed and fiber traits.
• GhMML3_A12 and its associated NAT/siRNA pathway represent a significant discovery for understanding and potentially manipulating cotton fiber development.