CANDIDATE GENE SELECTION IN Pinus radiata - FINDING THE NEEDLES IN THE HAYSTACK

¹ Forest Research, Private Bag 3020, Rotorua, New Zealand

² USDA Forest Service, Southern Institute of Forest Genetics, Saucier, MS 39574, USA

We are interested in identifying and characterising genes that are involved in cell wall formation. For this purpose, we have developed a strategy for candidate gene selection that involves a screen for differential gene expression and a quantitative confirmation of that expression difference using real-time PCR. This is followed by identification of polymorphisms in selected genes to investigate possible associations with variation in juvenile wood density (JWD), using a combination of QTL and linkage disequilibrium mapping. Top candidates can then be selected for further functional analysis. We have developed and employed a modified differential display technique (CAGE) that enables small subsets of cDNA to be analysed at one time (Cato et al, in prep.). Using this technique, we have identified approximately 450 genes that are show differential expression between mature and juvenile cambium and developing xylem tissue collected from 24 year-old Pinus radiata trees. To date, 60 of these genes have been further investigated by real-time PCR, with 80% confirmed with differential expression (comparison-wise p-value < 0.05). Expression differences ranged from 1.3-fold to 17.6-fold between tissues. Currently, 12 of the 450 genes have been mapped in a large QTL pedigree and investigated for co-localisation with juvenile wood density (JWD) QTL. Eight of these 12 genes have had their differential expression confirmed using real-time PCR. Seven genes mapped to regions with moderate-strong QTL associations, with another three with weaker associations. At least one polymorphisms from each of three genes have been genotyped on a 1950-tree association population, but to date none have shown any association with JWD.