Insight into growth and wood properties based on QTL and eQTL mapping in Populus deltoides ‘Danhong’ × Populus simonii ‘Tongliao1’

Abstract

Poplar is a short-rotation cultivated energy tree species, and analysis of genetic regulation of gene expression at the seedling stage is important for understanding phenotypic variation in growth rate and wood quality. However, the genetic regulation of xylem gene expression is still poorly understood. We determined transcriptomes of developing xylem of Populus deltoides ‘Danhong’, P. simonii ‘Tongliao1’ and F1 hybrids of them to explore the variations in the landscape transcriptome and its genetic basis. Through quantitative trait locus (QTL) and expression QTL (eQTL) analysis, we identified 237 QTLs, 48,019 cis-eQTLs and 2,184,889 trans-eQTLs contributing to the whole-genome transcriptome variation in poplar. Trans-acting effects play major role in expression regulation. We identified 38 eQTL hotspots, among which the A/T base mutation in PdCaM247 3′UTR in hot12654 influenced the wood basic density and regulated the expression of QTL major genes (YEATS and IQD32) and secondary cell wall related genes. Transgenic poplar with overexpressing PdCaM247 presented an increase of the secondary xylem. Yeast two-hybrid analysis revealed that PdCaM247 interacted with the secondary cell wall regulator MYB156. This study generates a large genetic resource for studying xylem development and provides new insights into the genetic basis of secondary cell wall regulatory networks.