Unique starch biosynthesis pathways in wild rice revealed by multi-omics analyses.

Area of Science:

• Genetics and Plant Breeding
• Molecular Biology
• Agricultural Science

Background:

• Australian wild rice species (AWS) exhibit distinct starch properties, including slow digestibility.
• The genetic and transcriptomic basis for these unique starch characteristics in AWS is not well understood.
• Starch-synthesis-related genes (SSRGs) play a crucial role in determining starch physiochemical properties.

Purpose of the Study:

• To comparatively analyze genomic and transcriptomic variations of 72 SSRGs in AWS and domesticated rice.
• To elucidate the influence of these variations on starch physiochemical properties and evolutionary pathways.
• To identify valuable AWS haplotypes for improving starch quality in cultivated rice.

Main Methods:

• Comparative analysis of 72 SSRGs across two AWS (O. meridionalis, O. rufipogon) and the domesticated rice gene pool.
• Transcriptome analysis to identify differential splicing and gene expression patterns during seed development.
• Comparative genomics to trace the evolutionary origins of key starch synthesis genes.

Main Results:

• Most SSRGs are highly expressed in early seed development stages.
• Starch synthesis pathways in Nipponbare and O. rufipogon are more similar than in O. meridionalis.
• AWS showed higher expression of GBSSI, SSIIa, and BEIIb, correlating with higher amylose content and gelatinization temperature.
• Asian domesticated rice evolved from single ancestral alleles for GBSSI and SSIIa, but two BEIIb alleles originated from wild progenitors.
• Higher expression of GBSSI, BEI, and SSIIIa in O. meridionalis contributes to slower starch digestibility.

Conclusions:

• Comparative genomics reveals the evolutionary trajectory of starch synthesis genes during rice domestication.
• AWS possess valuable SSRG haplotypes, particularly from O. meridionalis, that confer desirable slow starch digestibility.
• These findings offer a pathway for leveraging wild rice genetic resources to enhance starch quality traits in cultivated rice varieties.