Introgression of cultivar genes into wild carrot populations

Authors: Brunet, Johanne; PALMIERI, 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: 1/14/2020
Citation: Brunet, J., Palmieri, L. 2020. Introgression of cultivar genes into wild carrot populations [Abstract]. Plant and Animal Genome Conference. Available: https://plan.core-apps.com/pag_2020/abstract/374270e1-b407-43a2-a59d-46475a29fc44.

Interpretive Summary: N/a

Technical Abstract: Wild carrots are widespread in the USA, can be weedy and have been declared invasive in some states. Wild and cultivated carrots can easily hybridize as they are commonly found in close physical proximity and belong to the same species. Cultivar genes are introduced into wild carrot populations via pollinator-mediated gene flow and can spread within and among wild populations in a process called introgression. The extent of cultivar genes 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 magnify the invasiveness of wild carrots. To address introgression of cultivar genes into wild carrot populations, we sampled four wild carrot populations near (< 300m) and four far away (> 1000m) from cultivated carrots. In addition, we sampled wild populations at incremental 300m distances up to 1800m along three transects between one of the near and one of the far populations. Leaf tissue was sampled from 20 individuals per population, DNA was extracted and single nucleotide polymorphisms (SNPs) were identified against the carrot genome following genotyping by sequencing. We used fastSTRUCTURE on the SNP data to determine the genetic structure of the far and near wild populations, and the genetic structure of the cultivars grown at the West Madison Agricultural Research Station and the near and far wild populations. Cultivated and wild carrots were genetically differentiated. Moreover, near wild populations were more genetically diverse than far wild populations. To identify hybrids between cultivated and wild carrots, we ran STRUCTURE with 2 genetic clusters (K=2), forcing the cultivars as K=1 and the far wild populations as K= 2. We ran these analyses first on the near populations and then on all populations in the transects. We detected hybrid individuals in near wild populations. These results start addressing the spread of cultivar genes into wild carrot populations. The next steps will include pursuing these analyses on a larger scale while also determining whether specific regions of the genome are more prone to introgression.