Exploring the genetic basis of heterosis in eucalypt growth based on transcriptome analysis

The fundamental way to solve the problems of a Limited interspecific gene pool, poor stress resistance, and low yield in Chinese eucalypt plantations is to use the Heterosis derived from the eucalypt gene pool to select new varieties with rich genotypes. In order to reveal the genetic mechanism of the formation of Heterosis in eucalypt growth, based on previous research on the relationship between eucalypt heterosis and parental combining ability, we selected two artificial hybrids 18H167 (T15 × U3423) and 19H74 (U3423 × U6) with significant differences in birth length and similar parental relationships as the research objects. Transcriptome analysis using RNA-seq technology revealed correlations between gene expression levels that indicated the male parent had a greater impact on the heterosis of eucalypt growth. Based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, GSEA (Gene Set Enrichment Analysis) enrichment and WGCNA (Weighted Gene Co-expression Network Analysis) analysis identified 6 pathways and 8 Hub genes. The biological functions of these pathways involve resistance ability, mainly summarized as ribosomal subunits, extracellular regulatory mechanisms, and three amino acid synthesis pathways. We believe that one or several genes with altered expression levels in candidate pathways, either individually or in combination, directly regulate the growth of eucalypt or indirectly affect growth through adaptation to environmental stress. AS (Alternative Splicing) analysis showed that the AS events of the two hybrids were significantly higher than those of their parents, with SE (Skipped Exon) events possibly being related to growth disadvantages and RI (Retained Intron) events more likely to be related to growth advantages. This study provides a more in-depth exploration of the formation mechanism of heterosis in eucalypt growth and adds Python code to speed up the process, which are expected to guide the selection of parents in eucalypt hybrid breeding. The discovery of genetic mechanisms of heterosis related to growth provides genetic information for eucalypt genome annotation and molecular marker assisted breeding.