BioMatNet Item: QLK3-2002-01973 - Developing single nucleotide polymorphism (SNP) markers for adaptive variation in forest trees (TREESNIPS)

[BioMatNet Database - FP5 Quality of Life Programme]

QLK3-2002-01973
Developing single nucleotide polymorphism (SNP) markers for adaptive variation in forest trees (TREESNIPS)

Contacts

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Forestry : Quality of Life - 3. The Cell Factory

Type of Project	Shared Cost Research
Contract No	QLK3-2002-01973
Total Cost
EC Contribution	1,957,622 EUR
Start Date	01-10-2002
Duration	48 Months

Abstract

The availability of efficient sequencing methods has made it possible to use a new class of markers based on polymorphism at single nucleotide sites in functional genes. We propose to develop these techniques in trees and to test their use in finding markers in a set of neutral control genes and a set of genes potentially underlying adaptive variation in phenotypic traits responsible for adaptation to local climates. The markers in Scots pine, Norway spruce, Maritime pine and oak will be useful to managers of genetic resources, for conservation genetics and for tree breeding.

Objectives

The goal is to develop markers on single nucleotide polymorphism (SNP) in a set of candidate genes potentially related to adaptation to the local climatic conditions and to existing broad-scale climatic gradients. Climatic conditions such as length of growing season or water availability will be considered for four species, Scots pine, Norway spruce, Maritime pine and oak. The other set of genes that will be studied will be chosen so that they are unrelated to the climatic gradients, and therefore could serve as a set of neutral control loci. The project will also develop theory and statistical methods for establishing the role of the candidate genes in forest trees that are out-crossing species with high between-population divergence. The SNPs methods developed in this project will serve all future work in this area of forest trees.

Activities

The work starts with finding a list of suitable neutral control and candidate genes (about 10) plus 10 per species/trait combination based on:

available literature on the physiology and gene expression of candidate genes.
sequence databases in Arabidopsis, the four species studied here and other species.

These loci will then be placed on existing linkage maps' pedigrees. To provide estimates of quantitative genetic parameters, about 20 populations per species will be used for phenotypic characterisation either in field of greenhouse trials. An initial study on about 30 alleles per species from populations range-wide will provide initial information on nucleotide diversity patterns and serve as basis for choice of a more limited set of loci for the second stage. For this more limited set of loci, a few SNPs will be characterised in about 20 individuals in each of the 20 populations. Theoretical studies and simulations will be used to find the most efficient methods for finding the nucleotide sites responsible for the high level of quantitative trait differentiation in these species. The implications for management of gene resources, gene conservation, tree breeding and silviculture will be assessed.

Deliverables

A list of candidate and control genes, map of the genes, description of the phenotypic differentiation, statistics for nucleotide diversity in initial set of loci, SNP frequency and distribution for a limited set of loci, and a comparison of genotypic and phenotypic differentiation will be provided. Expected results include nucleotide diversity statistics for each species, potentially a list of loci and nucleotide sites for adaptive variation and statistical methods for future work.

Contacts

Coordinator

Outi SAVOLAINEN / University of Oulu Department of Biology / FINLAND

Participant