Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar

• R _US is a major dominant gene controlling quantitative resistance, inherited from Populus trichocarpa, whereas R ₁ is a gene governing qualitative resistance, inherited from P.deltoides. • Here, we report a reiterative process of concomitant fine-scale genetic and physical mapping guided by the P. trichocarpa genome sequence. The high-resolution linkage maps were developed using a P.deltoides×P. trichocarpa progeny of 1415 individuals. R _US and R ₁ were mapped in a peritelomeric region of chromosome 19. Markers closely linked to R _US were used to screen a bacterial artificial chromosome (BAC) library constructed from the P. trichocarpa parent, heterozygous at the locus R _US. • Two local physical maps were developed, one encompassing the R _US allele and the other spanning r _US. The alignment of the two haplophysical maps showed structural differences between haplotypes. The genetic and physical maps were anchored to the genome sequence, revealing genome sequence misassembly. Finally, the R _US locus was localized within a 0.8-cM interval, whereas R ₁ was localized upstream of R _US within a 1.1-cM interval. • The alignment of the genetic and physical maps with the local reorder of the chromosome 19 sequence indicated that R _US and R ₁ belonged to a genomic region rich in nucleotide-binding site leucine-rich repeat (NBS-LRR) and serine threonine kinase (STK) genes.