| Loblolly pine (Pinus taeda) is the most commercially important forest tree species in US. Fungal diseases of loblolly pine cost c. {dollar}75 million to {dollar}130 million to the forestry industry every year. Despite decades of research on fungal disease resistance in conifers, the genetic basis of the resistance mechanism of the host stays elusive to this day. My objective was to dissect the genetic basis of loblolly pine resistance against these pathogens using a novel candidate gene association mapping approach. A total of 42 candidate loci were identified and screened for Single Nucleotide Polymorphisms (SNPs) that might influence host's resistance to fungal diseases. Subsequently, the list of candidates was expanded to 57, with the addition of candidate genes identified to contribute to drought tolerance, for which SNP data was readily available. Selected SNPs were tested for their relevance to the variation observed in the resistance phenotypes via association testing of these polymorphisms over a family-based association population of 960 individuals.; More then 750,000 bps of total sequence data was generated, over 32 individuals, covering about 25Kb of the Pinus taeda genome, over 42 loci. Average intron length was 143 bps, while average exon length was 217 bps. A total of 524 SNPs were discovered within 42 loci, generating an average nucleotide sequence diversity of thetaw = 0.00546 with a SNP density of approximately, one SNP per every 50 bps. Furthermore, to investigate patterns of sequence divergence in Pinus, about 20 Kb of polymorphism data was compared between Pinus taeda and three other Pinus species: Pinus elliottii, Pinus radiata, and Pinus sylvestris. The patterns detected demonstrated large variations within genomes and among species, and in some cases significant deviations from neutral expectations. A total of nine loci was identified to influence pitch canker resistance, explaining about 9--23% of the variance observed in disease resistance of Pinus taeda to necrotrophic fungus Fusarium circinatum; and four loci have been identified to influence relative risk of fusiform rust disease of Pinus taeda caused by biotrophic fungus Cronartium quercuum ssp. fusiforme . |
