Comparative Genomics of Acacia auriculiformis and Acacia mangium

Acacia auriculiformis x A. mangium hybrid (2n=26) is emerging as an important forest tree for pulpwood production in Southeast Asia. Marker Assisted Selection is currently applied in Acacia breeding programmes to increase the productivity of forest plantation in shorter time. Recently Next Generation Sequencing has facilitated the discovery of Single Nucleotide Polymorphism (SNP) markers via transcriptome sequencing of A. auriculiformis and A. mangium. Besides linkage map construction, mapping of these sequence-based markers will allow comparative study with model species and provide first insight into genome organization and evolution of Acacia. A total of 123 Acacia hybrid F₁ progenies from AA6 x AM20 population were used in linkage mapping analysis. The paternal and maternal linkage maps were constructed out of 239 and 163 SNP markers respectively using Joinmap. Thirteen linkage groups ranging from 22.9 cM to 156.6 cM were identified in both linkage maps. The total lengths of the paternal and maternal maps were 1086.7 cM and 822.3 cM with an average marker interval of 4.5 and 5.0 cM respectively. The ordering of anchor loci between both linkage maps were consistent suggesting both species shared high similarity in genome organization. Comparative genomics of Acacia with model legume Medicago truncatula revealed high gene conservation and significant macrosynteny. Two Acacia linkage groups shared extensive colinearity with M. truncatula chromosome 6 which contains NBS-LRR megacluster. This study demonstrated the first comparative genomics study between Mimosoideae and Papilionoideae subfamilies that diverged about 55 million years ago.