ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes

Area of Science:

• Plant Molecular Genetics
• Genomics
• Biotechnology

Background:

• Expressed sequence tags (ESTs) are useful for discovering single nucleotide polymorphisms (SNPs) in humans, but their application in higher plants is limited.
• Sugarcane (Saccharum officinarum) genetics research can benefit from exploring ESTs for polymorphism discovery.

Purpose of the Study:

• To investigate the utility of sugarcane ESTs for identifying single nucleotide polymorphisms (SNPs) in alcohol dehydrogenase (Adh) genes.
• To characterize the Adh gene family in sugarcane and assess sequence variation.

Main Methods:

• Utilized a database of ~250,000 sugarcane ESTs to identify sequences encoding alcohol dehydrogenases (Adh).
• Partitioned ESTs into paralogous genes (Adh1 and Adh2) and validated using external data, including sorghum.
• Analyzed sequence alignments to detect single nucleotide polymorphisms (SNPs) and insertion-deletions (indels).

Main Results:

• Identified 219 Adh-encoding sequences, representing 178 distinct cDNAs from four cultivars.
• Discovered 37 highly reliable SNPs across three Adh genes, with a mean occurrence of one SNP per 122 base pairs in coding regions.
• Observed eight insertion-deletions, exclusively in untranslated regions.

Conclusions:

• Sugarcane ESTs are a rich source of sequence polymorphism, particularly for Adh genes.
• The findings demonstrate the potential of EST data for developing novel molecular marker tools in sugarcane.
• Further collection and analysis of EST data are recommended for advancing sugarcane genetic research.