Integrating genomics and quantitative genetics for discovery of genes that regulate bioenergy traits in woody species

Wood can provide a renewable source of energy to sustain our economic development. To meet the increasing demand for wood and bioenergy without harvesting natural forest ecosystems, it is critical that both productivity and wood quality of fast-growing, short-rotation plantation forests be improved. Eucalyptus and Populus are the fastest growing woody species in tropical and temperate conditions, respectively. To efficiently improve these species, it is important that genetic and genomic resources are accessible to assist breeding and allow identification of genes regulating bioenergy traits. With the genome sequenced and hundreds of thousands of expressed sequence tags (ESTs), Populus has more developed genomic resources than Eucalyptus. To address this limitation in Eucalyptus and allow comparative genomics with Populus, we utilized 454 sequencing technology to generate 148 Mbp of expressed sequences and survey the nucleotide diversity in >2,000 genes of Eucalyptus grandis [Chapter 2 -- published in BMC Genomics, 2008]. This work is contributing to the annotation of the forthcoming Eucalyptus genome sequence. Working with poplars, we have identified one genomic region (QTL) on chromosome XIII that is significantly associated with biomass growth and composition, based on relative levels of wood cellulose and lignin [Chapter 3 -- published in New Phytologist, 2009]. This QTL explains 56% of the heritable variation in cellulose to lignin ratio, as well as 20-25% of the heritable variation of several productivity traits, including stem diameter and biomass accumulation in root and shoot. By integrating the multiple genomic resources available for Populus, we identified the gene cpg13 (carbon partitioning and growth in LG13) as the likely regulator underlying this QTL [Chapter 4]. Microarray analysis shows that the expression of cpg13 is cis-regulated, and highly correlated with levels of wood cellulose and lignin, as well as with the expression of genes in the phenylpropanoid pathway. Cpg13 has highly conserved homologues in all plant species sequenced so far, but their molecular function is currently unknown. Characterization of cpg13 is expected to illuminate the function of these homologues and to uncover the molecular mechanisms involved in the coordinate regulation of wood composition and tree growth.