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Tropical Pine Genomics


Tropical and subtropical pine tree species play an important role in South Africa’s bioeconomy and make up half of all the timber plantations in South Africa. Long generation times, late expression of complex traits and the large costs associated with traditional tree breeding trials, have stimulated an interest in the implementation of genomic technologies in pine tree breeding. However, until recently, there has been a lack of resources to analyze large numbers of DNA markers in pine trees, partly due to the enormous size of pine tree genomes (over 20 billion base pairs – seven times larger than human genomes). In 2020 the FMG Programme, together with the international tropical pine SNP Consortium, contributed to the development of a SNP genotyping array for tropical pine species and hybrids. The 50,000 (50K) Axiom 384-format SNP array (Jackson, Christie et al 2021) is currently being used to establish genomic reference profiles that will aid in species and hybrid identification. The first tropical pine genetic linkage maps have been constructed and we can now perform marker-trait association analyses for oligogenic traits, for example disease resistance traits, in the mapping pedigrees. For more complex traits, affected by many genes, for example tree volume or wood density, we can build genomic selection models which will aid in fast-tracking the pine breeding cycle. Finally, the SNP array together with future genome sequencing efforts in pine species, may enable the analysis and prediction of genotype by environment (GxE) interactions, which will allow us to make climate or environment-specific selections in the coming decades.

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