Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.
BACKGROUND
Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches.


RESULTS
The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait.


CONCLUSIONS
This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.
BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France.
Jérôme
http://orcid.org/0000-0002-0855-3828
J
Bartholomé
Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands.
Marco Cam
MC
Bink
Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands.
Joost
J
van Heerwaarden
BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France.
Emilie
E
Chancerel
BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France.
Christophe
C
Boury
BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France.|HelixVenture, Mérignac, France.
Isabelle
I
Lesur
North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC, United States of America.
Fikret
F
Isik
BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France.
Laurent
L
Bouffier
BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France.
Christophe
C
Plomion
D018744:DNA, Plant / Q000032:analysis; D056726:Genetic Association Studies / Q000379:methods*; D008040:Genetic Linkage; D028223:Pinus / Q000235:genetics / Q000502:physiology*; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
D018744:DNA, Plant