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Background  Linkage maps are useful tools for examining both the genetic architecture of quantitative traits and the evolution of reproductive incompatibilities. We describe the generation of two genetic maps using reciprocal interspecific backcross 1 (BC 1 ) mapping populations from crosses between  Iris brevicaulis  and  Iris fulva . These maps were constructed using expressed sequence tag (EST)- derived codominant microsatellite markers. Such a codominant marker system allowed for the ability to link the two reciprocal maps, and compare patterns of transmission ratio distortion observed between the two.    Results  Linkage mapping resulted in markers that coalesced into 21 linkage groups for each of the reciprocal backcross maps, presumably corresponding to the 21 haploid chromosomes of  I. brevicaulis  and  I. fulva . The composite map was 1190.0-cM long, spanned 81% of the  I. brevicaulis  and  I. fulva  genomes, and had a mean density of 4.5 cM per locus. Transmission ratio distortion (TRD) was observed in 138 (48.5%) loci distributed in 19 of the 21 LGs in BCIB, BCIF, or both BC 1  mapping populations. Of the distorted markers identified,  I .  fulva  alleles were detected at consistently higher-than-expected frequencies in both mapping populations.    Conclusions  The observation that  I. fulva  alleles are overrepresented in both mapping populations suggests that  I .  fulva  alleles are favored to introgress into  I .  brevicaulis  genetic backgrounds, while  I .  brevicaulis  alleles would tend to be prevented from introgressing into  I .  fulva . These data are consistent with the previously observed patterns of introgression in natural hybrid zones, where  I .  fulva  alleles have been consistently shown to introgress across species boundaries.

Transmission ratio distortion results in asymmetric introgression in Louisiana Iris