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Hybridization and Introgression
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Wild carrots are widespread in the USA, can be weedy and have been declared invasive in some states. We examined the population dynamics of wild carrot populations (Van Etten and Brunet, 2017) and the genetic structure and domestication of carrot (Iorizzo et al. 2013). We reviewed gene flow in carrots (Mandel and Brunet, 2019 book chapter in ‘The carrot genome, Compendium of Plant Genomes’) and examined potential gene flow from cultivar genes into wild carrot populations near a carrot breeding site in Wisconsin (Palmieri et al. Acta Horticulturae 2019). More recently we extended our study of introgression of cultivar alleles into wild carrot populations throughout more regions in the United States (Hernandez et al. in prep.). The extent of cultivar alleles into wild US carrot populations is a critical question because, with the deployment of new gene editing technologies, the likelihood that genetically modified carrot cultivars will be released in the future has increased and some of these cultivar alleles could increase the invasiveness of wild carrots. We use genotyping by sequencing (GBS) and SNPs data to quantify the pattern of introgression of cultivar genes into wild carrot populations. We are also determining whether specific regions of the genome are more prone to introgression than others.

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Elm Hybridization and Dutch Elm Disease

We determined the pattern of hybridization between the native Red elm, Ulmus rubra, and an invasive exotic species, the Siberian elm, Ulmus pumila in Wisconsin. We developed species-specific microsatellite markers that permitted the genetic identification of putative hybrid individuals in contact zones between the two parental species (Zalapa et al. 2008, Molecular Ecology Resources); we described the genetic diversity of U. pumila present at the UW Arboretum in Wisconsin and planted from seeds originally collected throughout China (Zalapa et al. 2008, Genome). We confirmed genetically the presence of hybrids between U. pumila and the native U. rubra and identified a pattern of introgression biased towards U. pumila (Zalapa et al. 2009, American Journal of Botany). Finally, we established the widespread presence of hybrids in naturalized U. pumila populations in Wisconsin and beyond (Zalapa et al. 2010, Evolutionary Applications). In addition, we collaborated with Dr. Alberto Santini, a forest plant pathologist in Italy, to examine patterns of hybridization between U. pumila and a native European elm, Ulmus minor (Brunet et al. 2013, Biological Invasions). Our results are raising serious concerns about the long-term survival of native elm species in the U.S. and potentially Europe. A collaboration with a German PhD student examined the extent of intra-specific hybridization in elm (Hirsch et al. 2017, Biological Invasions). Finally, we examined the impact of Dutch elm disease (DED) on the genetic diversity and level of genetic differentiation among populations of the native Slippery elm, U. rubra, in Wisconsin (Brunet et al. 2016, Conservation Genetics) and determined that DED did not decrease the genetic diversity or increase the levels of genetic differentiation among populations of Slippery elm and other native elm species (Brunet and Guries, 2017, Proceedings of the American Elm Restoration Workshop 2016).