Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed

Area of Science:

• Plant Molecular Biology
• Genetics and Genomics
• Crop Science

Background:

• Yellow seed coat color in rapeseed (Brassica napus) is a desirable trait associated with enhanced oil content and meal quality.
• Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism influencing plant development and cellular differentiation.

Purpose of the Study:

• To identify novel transcripts and isoform-level differences associated with seed coat color variation in Brassica napus.
• To investigate the role of alternative splicing in the development of yellow versus black seed coats in rapeseed.

Main Methods:

• Comparative analysis of 31 RNA-sequencing libraries from yellow- and black-seeded Brassica napus at five developmental stages.
• Identification and analysis of alternative splicing events, with a focus on intron retention.
• Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene modules associated with seed color.

Main Results:

• Alternative splicing events were largely similar between seed types, with intron retention being a predominant pattern.
• Alternative splicing predominantly occurred during early and mid-seed development stages.
• WGCNA identified two key modules significantly associated with seed color, highlighting differentially alternatively spliced (DAS) genes in the flavonoid pathway (e.g., TT8, TT5, TT12, AHA10, CHI, BAN, DFR) and an RNA-binding family protein gene (BnaC03g23650D).

Conclusions:

• Alternative splicing, particularly of flavonoid pathway genes and RNA-binding proteins, plays a crucial role in determining seed coat color in Brassica napus.
• The identified candidate DAS genes provide potential targets for marker-assisted selection and breeding programs to develop stable yellow-seeded rapeseed varieties.
• This research offers valuable insights into the molecular mechanisms underlying seed coat color formation in rapeseed.