Articles
Genetic markers to detect introgression of cultivar genes in wild carrot populations
Article number
1264_20
Pages
165 – 174
Language
English
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, 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 been 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 further away from the breeding site (3.3-20.8 km). 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 population structure of wild and cultivated carrots and then only the wild carrot.
We detected strong genetic differences between cultivated and wild carrots and between the near wild and far wild carrot populations.
We identified markers capable of detecting introgression by comparing the gene frequencies of these SNPs between the far wild, 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 of introgression.
Cultivar genes may then spread within and among wild carrot populations, 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 been 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 further away from the breeding site (3.3-20.8 km). 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 population structure of wild and cultivated carrots and then only the wild carrot.
We detected strong genetic differences between cultivated and wild carrots and between the near wild and far wild carrot populations.
We identified markers capable of detecting introgression by comparing the gene frequencies of these SNPs between the far wild, 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 of introgression.
Authors
L. Palmieri, S.L. Ellison, D. Senalik, P.W. Simon, J. Brunet
Keywords
Daucus carota, genotyping by sequencing, population structure
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