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

Abstract

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.

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

“…Most of the SNP-based studies performed within the Apiaceae family were mainly aimed at safeguarding or reconstructing the phylogenetic relationship and the geographical origin of species (e.g., D. carota [ 68 , 69 , 70 ], Erigenia bulbosa [ 71 ]) or tribes (e.g., Scandiceae [ 72 ]). With the exception of few cases, namely Carum carvi [ 73 ], D. carota [ 74 ] and Foeniculum vulgare [ 75 ], the use of SNPs for breeding purposes remains limited.…”