Investigating a low cost SNP genotype method in Pinus taeda

George Khan

Abstract

Understanding the genetic basis of population divergence and adaptation is an important aspect of forest genetic studies. Studying genetic markers have contributed greatly to the understanding of gene flow, hybridization, population structure, and genetic movement within species. In the forest tree production industry, genetic markers may be very useful for selective breeding to improve productivity and quality of trees planted for the purposes of wood production. A Single-Nucleotide Polymorphism (SNP) is a DNA sequence variation occurring when a single nucleotide differs between members of a species. These SNPs are potentially the best type of genetic marker because of their abundance in the genome and their association with genes that affect adaptive traits and susceptibility to disease. In this study we explore a low cost open source SNP genotyping protocol that use array based technology for assessing SNPs in 384 individuals. We are currently testing for the presence of the cad-n1 mutant allele in these 384 individuals in Pinus taeda, the most important tree species for production forestry in the southeastern US. We already have data on these individuals to use as a positive control to make sure the new method works and gives accurate results.

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Goals

The short-term goals of this research project are to survey fragments of genes in two individuals of each of a number of pine species for DNA sequence variation using the above mentioned methods, and then to analyze allele frequencies of a selected subset of polymorphic nucleotide markers from each species. The expected outcome is identification of species-specific SNPs useful for hybrid testing.

The long-term goals of this type of research are to develop and test efficient methods for discovery and analysis of species-specific SNP variation, to understand relationships between genetic variation and phenotypic variation with groups of closely related species, and to characterize the extent of gene flow between related populations.

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