Introgression of cultivar genes into wild carrot populations

Authors: Brunet, Johanne; PALMEIRI, LUCIANO - Oak Ridge Institute For Science And Education (ORISE)

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/11/2019
Publication Date: 1/15/2019
Citation: Brunet, J., Palmeiri, L. 2019. Introgression of cultivar genes into wild carrot populations [Abstract]. Plant and Animal Genome Conference. Available: https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/35546.

Interpretive Summary:

Technical Abstract: Wild carrots are widespread in the USA, can be weedy and have been declared invasive in some states. Wild and cultivated carrots are commonly found in close proximity and can easily hybridize. Following their introduction into wild populations via hybridization, cultivar genes can spread both within and among populations, a process called introgression. The extent of cultivar gene introgression into wild US carrot populations has not been quantified. This 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 genes could increase the invasiveness of wild carrots. We have previously compared the genetic diversity and genetic differentiation of four wild carrot populations located near and four located far away from cultivated carrots and found greater genetic differentiation and genetic diversity in the wild carrot populations in close proximity to cultivated carrots. This study also identified single nucleotide polymorphisms (SNPs) with great potential to detect introgression. In the current study, we further examine the pattern of introgression of cultivar genes into wild carrot populations. We sampled populations at incremental 300 meter distances along a line between one of the near and one of the far populations (near or far away from cultivars) to a distance up to 1800 meters. Leaf tissue was sampled from 20 individuals per population. This sampling process was repeated for three sets of near and far populations. We extracted DNA from the leaf tissue and performed genotyping by sequencing (GBS). We identified single nucleotide polymorphisms (SNPs) from the combined set of wild populations. We used fastSTRUCTURE to examine the population genetic structure of these wild carrots. First, we only evaluated the four populations near and four populations far away from cultivars. Second, we analyzed the populations within each of the three 1800 meter lines between a near and a far populations; we analyzed each of the three lines separately. Lastly, we combined all populations. In addition, we calculated isolation by distance for populations at increasing geographic distances from cultivated carrots. We first used all SNPs identified and then only a subset of the SNPs predicted to be good detectors of introgression from a previous study. These results will increase our understanding of the pattern of spread of cultivar genes into wild carrot populations. This information could guide the design of methods to reduce the spread of cultivar genes into wild carrot populations and help prevent potential negative impacts such as an increased invasiveness of wild carrot populations.