Acacia mangium and A. auriculiformis are the most popular Acacia species planted in Southeast Asia for timber and pulp production. The ASEAN region has an estimated 600,000 hectares of plantations of these tropical Acacia species and there is a growing demand for improved planting materials, particularly with improved lignin quality for pulping.

Discovery of genes involved in wood formation of Acacia hybrid (A. auriculiformis x A. mangium) was approached through the analysis of Expressed Sequence Tags (ESTs). A cDNA library with a size of 7000 clones was constructed from inner bark tissues of an Acacia hybrid. From this cDNA library, a total of 6415 ESTs were generated. Twenty five ESTs were found to represent enzymes involved in the biosynthesis of lignin and cellulose. Six genes involved in lignin biosynthesis were identified. They were phenylalanine ammonia lyase (PAL), caffeoyl-coenzyme A O-methyltransferase (CCoAOMT), caffeate O-methyltransferase (COMT), cinnamyl-alcohol dehydrogenase (CAD), cinnamoyl coenzyme A reductase (CCR), and cinnamate 4-hydroxylase (C4H). The full-length cDNA sequences of these lignin genes have been obtained with work on isolation, sequencing and annotation of their full length genomic sequence in progress. Apart from the lignin genes, 6 other genes involved in cellulose and hemicellulose syntheses were also identified in the Acacia hybrid EST database. Transcript profiling and functional analysis have been conducted for some of these lignin and cellulose genes to understand their expression in different tissues and role in lignin and wood formation.

Two Acacia hybrid mapping populations segregating for fibre length and wood density traits separately and two types of polymorphic molecular markers i.e. simple sequence repeats (SSRs) and cleaved amplified polymorphic sequences (CAPS) were developed for construction of genetic linkage mapping and QTL analysis.

A total of 174 SSR markers were developed from 5' anchored polymerase chain reaction technique and 93 markers from enrichment method. The new primers with additional six primers developed earlier from A. mangium were used to screen polymorphisms on four parental trees of the wood density and fibre length crosses. For the development of CAPS, a total of 405 primers were designed based upon 315 EST sequences related to wood formation. About 156 primers successfully amplified specific products. The 156 specific primers were used for screening restriction-site polymorphisms using 38 restriction enzymes on the four parental trees.

Some SSR markers showed polymorphisms in one cross but were monomorphic in another cross and vice versa. In total, 31 polymorphic SSR markers in the wood density cross and 22 polymorphic markers in the fibre length cross were obtained. A total of 167 markers were found to be monomorphic. The restriction-site polymorphism screening in parental trees resulted in seven polymorphic CAPS markers in the wood density cross and six polymorphic CAPS markers in the fibre length cross. About 152 CAPS markers were found to be monomorphic in the parental trees. The polymorphic SSR and CAPS markers were used for linkage analysis in 190 F1 progenies for both crosses.

Genetic linkage map comprising of 15 SSR and 2 CAPS loci in five linkage groups for the wood density cross was constructed. The linkage groups ranged in size from 8.2 to 61.7 centimorgan (cM) and the total length was 155.5 cM. For the fibre length cross, genetic linkage map comprised of 10 SSR and 5 CAPS loci in six linkage groups. The linkage groups ranged in size from 3.0 to 26 cM and the total length was 86 cM. The C-value of Acacia hybrid is 0.675 pg and the estimated total length of Acacia hybrid genome will be 675cM. Hence, the existing genome coverage is 12.7% (fibre length cross) to 23.0% (wood density cross). EST-SSR, amplified fragment length polymorphism (AFLP) and single nucleotide polymorphism (SNP) markers will be used to obtain a high density linkage map for the Acacia hybrid.

All the 190 full sib progenies from both crosses have been multiplied through micropropagation for field trials in January-December 2008 at 3 different sites i.e. Segamat, Johor, Lanchang, Pahang and Bintulu, Sarawak. QTL analysis for growth and wood quality traits will be carried out when the full sibs are 3-4 years.