Study on Leaf Rust Resistance in Populus Germplasm Resources Based on Multimodel GWAS and Selective Sweep Analysis

Leaf rust is one of the most destructive diseases affecting poplar trees worldwide. To develop disease-resistant varieties and identify novel resistance genes, this study investigated leaf rust in 135 Populus germplasm resources from different sections to screen for highly resistant clones. Selective sweep analysis and genome-wide association studies (GWAS) were employed to elucidate the genetic basis of leaf rust resistance. The results of the disease investigation revealed significant differences in rust resistance among different poplar clones. Clones such as P. alba, Populus 'Qinbaiyang1', and P. alba 'Yx-2' from the section Populus exhibited high resistance, whereas clones from the section Aigeiros and hybrids between sections showed substantial variation in resistance. Notably, segregation of leaf rust resistance was observed in certain hybrid combinations within or between sections. Cross-population composite likelihood ratio (XP-CLR) analysis identified 388 positively selected regions. GWAS analysis of leaf rust resistance phenotypes was conducted using four single-locus models and two multilocus models, among which seven loci were detected by two or more models. Haplotype analysis and Sanger sequencing revealed a significant difference in disease resistance between different genotypes at the Chr13_14699534 locus. Upstream of this locus, we identified a gene, BBX29. qRT-PCR showed that the relative expression level of BBX29 was significantly lower in resistant clones than in susceptible clones. By integrating the results of GWAS and XP-CLR analyses, we identified six potential candidate genes. This study provides preliminary insights into the genetic mechanisms underlying poplar leaf rust and offers valuable genetic resources for breeding rust-resistant poplar varieties.