Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

Abstract

BackgroundIncreasing 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.ResultsThe 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.ConclusionsThis 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.

Single Nucleotide Polymorphism (SNP) markers associated with high folate content in wild potato species

“…It is often more rapid and cost-effective than traditional linkage mapping. Linkage and association mapping are complementary approaches and are more similar than often assumed [ 36 , 37 ].…”

Independent and Joint‐GWASfor growth traits inEucalyptusby assembling genome‐wide data for 3373 individuals across four breeding populations

“…Various studies attempted GWAS for growth traits in forest trees, namely in Populus (Porth et al ., ; Allwright et al ., ; Du et al ., ; Fahrenkrog et al ., ), Pinus (Bartholomé et al ., ; Lu et al ., ) and Eucalyptus (Cappa et al ., ; Müller et al ., ; Resende et al ., ). Despite the considerably large number of individuals used in our study for each population and for the combined dataset, our results suggested that much larger numbers will be necessary to identify discrete regions capturing larger fractions of the genetic variance of complex traits as indicated by simulations (Spencer et al ., ; Visscher et al ., ).…”

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

“…There have been conflicting reports on the genetic architecture of stem straightness in trees. For example, Bartholomé et al [63] detected QTLs that explained up to 5% of the total phenotypic variation of ST in maritime pine. Yang et al [64] found QTLs that explained up to 15% of the total phenotypic variation of the stem straightness of Pinus hybrids.…”