Genetic dissection of growth and wood properties in a nested, half-sib Eucalyptus hybrid pedigree

Abstract

Eucalyptus is important for the forestry industry due to its excellent growth and wood properties. In crop species, nested multi-parent populations have been used to increase the power and resolution of quantitative trait loci (QTL) detection. These populations have predominantly been used in species in which recombinant inbred lines can be generated and have not been fully exploited in outcrossing species such as Eucalyptus. To determine if multi-parent mapping approach can be used effectively for genetic dissection in Eucalyptus, we made use of an existing F1 hybrid trial series, consisting nine E. grandis pollen parents and eight E. urophylla seed parents. The population has many full-sib (FS) families nested within half-sib (HS) families and was planted across four different sites. The objectives of this MSc study were to i) construct genetic linkage maps of one E. grandis pollen parent and one E. urophylla seed parent of the multi-parent population, ii) analyse transmission ratio distortion of mapped markers in the F1 hybrid progeny to identify hybrid compatibility barriers, iii) map QTLs underlying growth and wood properties in the two pure species parental maps. We constructed framework genetic linkage maps for the E. grandis pollen parent and the E. urophylla seed parent. A total of 388 (E. grandis HS family, n = 349) and 422 (E. urophylla HS family, n = 367) single nucleotide polymorphisms (SNP) markers were included in the linkage maps resulting in an average marker density of 2.4 cM. Using the genetic linkage maps, we identified 15 and 23 QTLs underlying growth and wood properties for the E. grandis and E. urophylla HS family, respectively. We identified large to medium effect QTLs, with the percentage of variance explained ranging from 3.06% to 36.58%. We identified different QTLs across the sites which suggests that the traits are affected by genotype-by-environment interaction. We analysed segregation distortion of the markers included in the framework genetic linkage maps within HS families, FS families and sites. We found that there is a large amount of segregation distortion (between 0 – 29.38% distortion) and that the patterns of distortion varied for individual FS families planted across multiple sites and single sites with multiple FS families. We were also able to identify potential pre- and postzygotic barriers to hybrid compatibility through the analysis of segregation distortion of dead and living trees. Taken together, these results show that there are both parent specific interactions, that are dependent on the environment, which underlie hybrid compatibility. In this study, we applied an approach whereby genetic linkage maps can be constructed and QTL identified in an outcrossing multi-parent mapping population. We show that multi-parent populations hold promise for studying hybrid compatibility, as diverse founders are crossed resulting in a number of F1 hybrid progeny. The results of this study show that this approach can be applied in existing F1 hybrid breeding trials for more fine scale genetic dissection of complex trait variation as well as hybrid compatibility of E. grandis and E. urophylla.