Genetic markers to detect introgression of cultivar genes in wild carrot populations

Authors: PALMIERI ROCHA, LUCIANO - Oak Ridge Institute For Science And Education (ORISE); Ellison, Shelby; Senalik, Douglas; Simon, Philipp; Brunet, Johanne

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2019
Publication Date: 1/15/2020
Citation: Palmieri Rocha, L., Ellison, S.L., Senalik, D.A., Simon, P.W., Brunet, J. 2020. Genetic markers to detect introgression of cultivar genes in wild carrot populations. Acta Horticulturae. 1264:165-174. https://doi.org/https://doi.org/10.17660/ActaHortic.2019.1264.20.
DOI: https://doi.org/10.17660/ActaHortic.2019.1264.20

Interpretive Summary: Wild carrot or Queen Anne's lace is widespread in the USA, can be weedy and has been declared invasive in some states. Gene flow between cultivated and wild carrot is likely because cultivated and wild carrots belong to the same plant species (Daucus carota), flower at similar times and often grow in close proximity. Cultivar genes can get introduced and spread into wild carrot populations, a process called introgression. In this study we use genotyping by sequencing to identify genetic markers capable of detecting introgression of cultivar genes into wild carrot populations. We detected between 52 and 863 such markers depending of the group of cultivars used for comparison. These markers were dispersed over all 9 carrot chromosomes suggesting that there were no chromosome free from introgression. Despite the fact that the wild carrots were collected from a small geographic area, we still observed significant genetic differentiation between wild and cultivated carrots. We also observed more genetic diversity in the wild populations in close proximity to the cultivars relative to populations further away. This study identifies various genetic markers to detect introgression and indicates that introgression does occur in wild carrot populations in proximity to cultivated carrots. This information will benefit carrot farmers and the carrot industry together with scientists and people concerned about the spread of cultivar genes into wild carrot populations. It will also interest researchers that are looking to develop genomic methods to prevent introgression of genetically modified genes into wild carrot populations.

Technical Abstract: Wild and cultivated carrots easily hybridize and cultivar genes can infiltrate wild carrot populations when pollinators move pollen from cultivated to wild carrots or when cultivar seeds migrate into wild carrot populations. Cultivar genes may then spread within and among wild carrot populations in a process called introgression. Wild carrots are widespread in the USA, can be weedy, and have been declared invasive in some states. However, the extent of cultivar gene introgression into wild US carrot populations has yet to be quantified. The goal of this study is to identify genetic markers to detect the presence of cultivar genes in wild carrot populations. To reach this goal, we sampled leaf tissue from individuals in each of four wild carrot populations near a site that has been used to breed carrot cultivars for about 40 years. We also collected leaf tissue from individuals in wild carrot populations away from the breeding site. We extracted DNA and performed genotyping by sequencing (GBS) on these samples. We identified single nucleotide polymorphisms (SNPs) from the combined samples of cultivated and wild carrots. We used these SNPs to examine, using fastSTRUCTURE, the genetic structure of wild and cultivated carrots and then only wild carrot. We detected strong genetic differences between cultivated and wild carrots and between the wild carrots near vs. far from the breeding site. We identified markers capable of detecting introgression by comparing the gene frequencies of these SNPs between the far, near wild and cultivar groups. Depending on the cultivars used in the analyses, we detected between 52 and 863 such markers. These markers did not aggregate over some chromosomes but were dispersed over all nine carrot chromosomes, suggesting that no chromosome was free from introgression.