NUCLEOTIDE DIVERSITY, LINKAGE DISEQUILIBRIUM AND ADAPTIVE VARIATION IN NATURAL POPULATIONS OF LOBLOLLY PINE

¹ Environmental Horticulture, University of California, Davis CA 95616 and Center of Forest Research, INIA, PO Box 8111 28080 Madrid, Spain

² Environmental Horticulture, University of California, Davis CA 95616

³ Weyerhaeuser Company, Weyerhaeuser Technical Center, Tacoma WA 98477

⁴ Environmental Horticulture, University of California, Davis CA 95616 and Institute of Forest Genetics, USDA Forest Service, Davis CA 95616

Quantitative genetics has been widely applied to the analysis of adaptive traits in long-term common garden experiments. However, the molecular pattern underlying adaptation to changing environmental conditions is fairly unknown. With this objective in view, a candidate gene-based strategy was developed to detect natural adaptive variation for drought tolerance in loblolly pine (Pinus taeda L.). DNA samples from 32 megagametophytes (haploid tissue) were sequenced for ~20 drought tolerance related genes, including some, such as plp3-1 and dhn-1, where expression studies had been previously conducted. Based on this sample, collected mainly from the south-easternmost part of loblolly pine’s distribution, nucleotide diversity estimates were computed. Silent nucleotide diversity was high (0.0074) but nonsynonymous substitutions were relatively rare (0.0021). Haplotypes were identified and a set of SNPs (Single Nucleotide Polymorphisms) distinguishing the most common haplotypes and also those rare haplotypes containing nonsynonymous substitutions was selected. Screening of SNPs in a full-range sample (435 trees) provided relevant information about differential selection and adaptive processes related to drought tolerance in this economically important and widespread conifer species.