Systems genetics of wood formation in a Eucalyptus urophylla x E. grandis (UxG) nested association mapping (NAM) population.

Kleinhans, N.*, Naidoo, S., Christie, N., Myburg, A. A.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa

Systems genetics studies can be used to gain an understanding of the genetic basis of complex traits such as wood properties in Eucalyptus, and thereby inform the design of genomic breeding programmes. Most Eucalyptus systems genetics studies have focused on single biparental crosses (mapping families), but this provides a limited view of architecture across families. The main limitations to multi-family studies include the cost of NGS technologies and the lack of high-throughput methods for RNA isolation. We aim to elucidate the genetic architecture of wood property variation in a nested (multiparent) association mapping (NAM) population of Eucalyptus urophylla x E. grandis (UxG) hybrids consisting of four families. The first objective is to generate 400 transcriptomes for each family using a custom high-throughput RNA isolation method and Quantseq, otherwise known as 3’mRNA tag-seq, a cost-effective alternative for gene expression profiling in large multi-family studies. The second objective entails mapping quantitative trait loci (QTLs) for wood chemistry traits and expression QTLs (eQTLs) that may underlie these QTLs. The availability of fully phased haplogenomes (i.e. maternal and paternal genome assemblies) of the mapping parents allows us to infer eQTL haplotypes with greater accuracy by associating gene expression variation with parent-specific genomic variants. Finally, we will integrate this data into co-expression networks to shed light on the genetic regulation of wood formation in the Eucalyptus model. This study will greatly expand our knowledge of the complex genetic regulation of wood formation and aid in more informed Eucalyptus breeding strategies.

Keywords: QTL, eQTL, systems genetics, Eucalyptus, co-expression networks, wood formation