11/06/2009
Bionformatics Helps Identify Genes Associated with Plant Cell Wall Traits
The Science
The primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here researchers present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance.
Summary
The completion of the whole genome sequence of poplar (Populus) has made possible the use of bioinformatics and evolutionary methods to identify new candidate genes associated with plant cell wall traits. Researchers at DOE’s BioEnergy Science Center at the Oak Ridge National Laboratory have used information on the poplar genome structure and its duplication, quantitative trait locus mapping, and analysis of publicly available microarray data to reduce the thousands of poplar genes that could contribute to cell wall traits down to 15-20 candidate genes. These genes are now being tested experimentally to identify their functions. This research highlights how bioinformatics can help focus research in the most promising directions potentially reducing time consuming experimental methods for correlating genes with phenotype. The results will facilitate research to enhance plant biomass properties for more efficient conversion into biofuels.
References
Ranjan, P., T. Yin, X. Zhang, U. C. Kalluri, X. Yang, S. Jawdy, and G. A. Tuskan. 2010. “Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus,” Bioenergy Research, 172-82. DOI:10.1007/s12155-009-9060-z.