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Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence
Author(s) -
Yin T.M.,
DiFazio S. P.,
Gunter L. E.,
Jawdy S. S.,
Boerjan W.,
Tuskan G. A.
Publication year - 2004
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/j.1469-8137.2004.01161.x
Subject(s) - genetics , biology , linkage disequilibrium , locus (genetics) , genetic linkage , backcrossing , gene , amplified fragment length polymorphism , candidate gene , gene mapping , populus trichocarpa , sequence tagged site , allele , haplotype , genome , population , genetic diversity , chromosome , demography , sociology
Summary• In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa , we have mapped two resistance loci, MXC3 and MER , and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations. • We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun‐sequence data in the region containing markers linked to MXC3 . • The two loci were mapped to different linkage groups. Linkage disequilibrium for MXC3 was confined to two closely linked regions spanning 34 and 16 kb, respectively. The MXC3 region also contained six disease‐resistance candidate genes. • The MER and MXC3 loci are clearly distinct, and may have different mechanisms of resistance, as different classes of putative resistance genes were present near each locus. The suppressed recombination previously observed in the MXC3 region was possibly caused by extensive hemizygous rearrangements confined to the original parent tree. The relatively low observed LD may facilitate association studies using candidate genes for rust resistance, but will probably inhibit marker‐aided selection.