Identification of genes alternatively spliced in developing maize endosperm.

Area of Science:

• Plant Biology
• Molecular Biology
• Genetics

Background:

• Alternative splicing is vital for plant growth and development.
• Its role in maize endosperm development remains largely unexplored.

Purpose of the Study:

• To identify genes undergoing alternative splicing during maize endosperm development.
• To investigate the function of alternatively spliced genes in endosperm development.

Main Methods:

• RNA sequencing (RNA-seq) of maize endosperm from two inbred lines (Mo17 and Ji419) at different developmental stages (15 and 25 DAP).
• Identification and validation of alternatively spliced events, including intron retention (IR), using PCR and re-sequencing.
• Analysis of gene co-expression networks.

Main Results:

• Approximately 49,000 alternatively spliced events and 20,000 alternatively spliced genes were identified.
• 30 genes involved in amino acid and starch biosynthesis showed sample-specific IR and were co-expressed with known endosperm development genes.
• Intron retention in GRMZM2G005887 (cysteine synthase) was confirmed in Mo17 endosperm at 15 DAP, with regulatory elements in the retained fragment.

Conclusions:

• The identified 30 genes with IR are likely important for maize endosperm development.
• Alternative splicing, particularly IR in specific genes, plays a significant role in regulating maize endosperm development.