Mapping Quantitative Traits in Forest Trees

Quantitative trait loci for key defensive compounds affecting herbivory of eucalypts in Australia

* Formylated phloroglucinols (FPCs) are key defensive compounds that influence herbivory by mammals and arthropods in eucalypts. However, the genetic architecture underlying variation in their levels remains poorly understood. * Quantitative trait loci (QTL) analysis for the concentrations of two major FPCs, sideroxylonal A and macrocarpal G, was conducted using juvenile leaves from 112 clonally duplicated progenies from an outcross F2 of Eucalyptus globulus. * Two unlinked QTL were located for macrocarpal, while another unlinked QTL was located for sideroxylonal. The sideroxylonal QTL collocated with one for total sideroxylonal previously reported using adult Eucalyptus nitens foliage, providing independent validation in a different evolutionary lineage and a different ontogenetic stage. * Given the potential widespread occurrence of these QTL, their ontogenetic stability, and their impact on a range of dependent herbivores, it is possible that they have extended phenotypic effects in the Australian forest landscape.

Forest-tree population genomics and adaptive evolution

Forest trees have gained much attention in recent years as nonclassical model eukaryotes for population, evolutionary and ecological genomic studies. Because of low domestication, large open-pollinated native populations, and high levels of both genetic and phenotypic variation, they are ideal organisms to unveil the molecular basis of population adaptive divergence in nature. Population genomics, in its broad-sense definition, is an emerging discipline that combines genome-wide sampling with traditional population genetic approaches to understanding evolution. Here we briefly review traditional methods of studying adaptive genetic variation in forest trees, and describe a new, integrated population genomics approach. First, alleles (haplotypes) at candidate genes for adaptive traits and their effects on phenotypes need to be characterized via sequencing and association mapping. At this stage, functional genomics can assist in understanding gene action and regulation by providing detailed transcriptional profiles. Second, frequencies of alleles in native populations for causative single-nucleotide polymorphisms are estimated to identify patterns of adaptive variation across heterogeneous environments. Population genomics, through deciphering allelic effects on phenotypes and identifying patterns of adaptive variation at the landscape level, will in the future constitute a useful tool, if cost-effective, to design conservation strategies for forest trees.

Association genetics of complex traits in conifers

Association studies are becoming the experimental approach of choice to dissect complex traits in many organisms from humans to model plant systems. The candidate gene based-association approach has several important advantages for complex trait dissection in many coniferous forest tree species, including random mating and unstructured populations, adequate levels of nucleotide diversity, rapid decay of linkage disequilibrium, and precise evaluation of phenotype from clonal or progeny testing. Allele discovery using association approaches should lead to more-efficient methods of marker-assisted breeding and a deeper understanding of genetic adaptation in forest trees.

Detection and verification of quantitative trait loci for resistance to Dothistroma needle blight in Pinus radiata

Six related radiata pine ( Pinus radiata) full-sib families were used to detect and independently verify quantitative trait loci (QTLs) for resistance to Dothistroma needle blight, caused by Dothistroma septospora. The detection families had from 26 to 30 individuals each, and had either a common maternal (31053) or paternal (31032) parent; one family (cross 4) consisted of progeny from both parents, 31053 x 31032. Approximately 200 additional progeny from cross 4 were clonally replicated and planted at two sites, with at least five to seven ramets of each individual per site. Marker segregation data were collected from a total of 250 RFLP and microsatellite markers, and single factor ANOVAs were conducted separately for each family and marker. A number of putative associations were observed, some across more than one family. Permutation tests were used to confirm expected probabilities of multiple associations based on chance alone. Seven markers representing at least four QTLs for resistance to Dothistroma were identified as being significant in more than one family; one of these was significant at P<0.05 in three families and highly significant at P<0.01 in a fourth. Further confirmation was obtained by testing those markers that were significant in more than one of the detection families (or highly significant in cross 4) in the clonally replicated progeny from cross 4. Four QTL positions were verified in the clonal populations, with a total percent variation accounted for of 12.5.

Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mapping

A long-term series of experiments to map QTL influencing wood property traits in loblolly pine has been completed. These experiments were designed to identify and subsequently verify QTL in multiple genetic backgrounds, environments, and growing seasons. Verification of QTL is necessary to substantiate a biological basis for observed marker-trait associations, to provide precise estimates of the magnitude of QTL effects, and to predict QTL expression at a given age or in a particular environment. Verification was based on the repeated detection of QTL among populations, as well as among multiple growing seasons for each population. Temporal stability of QTL was moderate, with approximately half being detected in multiple seasons. Fewer QTL were common to different populations, but the results are nonetheless encouraging for restricted applications of marker-assisted selection. QTL from larger populations accounted for less phenotypic variation than QTL detected in smaller populations, emphasizing the need for experiments employing much larger families. Additionally, 18 candidate genes related to lignin biosynthesis and cell wall structure were mapped genetically. Several candidate genes colocated with wood property QTL; however, these relationships must be verified in future experiments.