On genetic diversity in caraway: Genotyping of a large germplasm collection

Caraway (Carum carvi) is a widespread and frequently used spice and medicinal plant with a long history of cultivation. However, due to ongoing climatic changes, the cultivation is becoming increasingly risky. To secure caraway cultivation in future, timely breeding efforts to develop adapted materi...

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Bibliographic Details
Published in:PloS one 2020-12, Vol.15 (12), p.e0244666-e0244666
Main Authors: von Maydell, Daniel, Lehnert, Heike, Berner, Thomas, Klocke, Evelyn, Junghanns, Wolfram, Keilwagen, Jens, Marthe, Frank
Format: Article
Language:English
Subjects:
Bayesian analysis
Biological diversity
Biology and Life Sciences
Biotechnology
Botanical research
Breeding
Caraway
Carum - genetics
Classification
Climate change
Cluster analysis
Clustering
Computer and Information Sciences
Crops
Cultivars
Cultivation
Distribution
Ecology and Environmental Sciences
Flow cytometry
Flowering
Flowers & plants
Genetic analysis
Genetic aspects
Genetic diversity
Genetic Variation
Genetics, Population
Genome, Plant
Genomes
Genotype
Genotyping
Genotyping Techniques
Germplasm
Herbal medicine
Horticulture
Medicinal plants
Medieval period
Methods
Phylogeny
Polymorphism, Single Nucleotide
Population
Population genetics
Population structure
Single-nucleotide polymorphism
Subpopulations
Variance analysis
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Summary:Caraway (Carum carvi) is a widespread and frequently used spice and medicinal plant with a long history of cultivation. However, due to ongoing climatic changes, the cultivation is becoming increasingly risky. To secure caraway cultivation in future, timely breeding efforts to develop adapted material are necessary. Analysis of genetic diversity can accompany this process, for instance, by revealing untapped gene pools. Here, we analyzed 137 accessions using genotyping by sequencing (GBS). Hence, we can report a broad overview of population structure and genetic diversity of caraway. Population structure was determined using a principal coordinate analysis, a Bayesian clustering analysis, phylogenetic trees and a neighbor network based on 13,155 SNPs. Genotypic data indicate a clear separation of accessions into two subpopulations, which correlates with the flowering type (annual vs. biennial). Four winter-annual accessions were closer related to biennial accessions. In an analysis of molecular variance, genetic variation between the two subpopulations was 7.84%. In addition, we estimated the genome size for 35 accessions by flow cytometry. An average genome size of 4.282 pg/2C (± 0.0096 S.E.) was estimated. Therefore, we suggest a significantly smaller genome size than stated in literature.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0244666