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Development of microsatellite markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a plant with a large and highly repetitive genome
ID Varga, Filip (Author), ID Liber, Zlatko (Author), ID Jakše, Jernej (Author), ID Turudić, Ante (Author), ID Šatović, Zlatko (Author), ID Radosavljević, Ivan (Author), ID Jeran, Nina (Author), ID Grdiša, Martina (Author)

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Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevis.) Sch. Bip.) is an outcrossing plant species (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repeatability and large genome (1C-value = 9.58 pg) our previous attempts to develop microsatellite markers using the traditional method were unsuccessful. Now we have used Illumina paired-end whole genome sequencing and developed a specific procedure to obtain useful microsatellite markers. A total of 796,130,142 high-quality reads (approx. 12.5× coverage) were assembled into 6,909,675 contigs using two approaches (de novo assembly and joining of overlapped pair-end reads). A total of 31,380 contigs contained one or more microsatellite sequences, of which di-(59.7%) and trinucleotide (25.9%) repeats were the most abundant. Contigs containing microsatellites were filtered according to various criteria to achieve better yield of functional markers. After two rounds of testing, 17 microsatellite markers were developed and characterized in one natural population. Twelve loci were selected for preliminary genetic diversity analysis of three natural populations. Neighbor-joining tree, based on the proportion of shared alleles distances, grouped individuals into clusters according to population affiliation. The availability of codominant SSR markers will allow analysis of genetic diversity and structure of natural Dalmatian pyrethrum populations as well as identification of breeding lines and cultivars.

Language:English
Keywords:Tanacetum cinerariifolium, Dalmatian pyrethrum, Asteraceae, genomic SSRs, microsatellite markers, SSR markers
Work type:Article
Typology:1.01 - Original Scientific Article
Organization:BF - Biotechnical Faculty
Publication status:Published
Publication version:Version of Record
Year:2022
Number of pages:11 str.
Numbering:Vol. 11, iss. 13, art. 1778
PID:20.500.12556/RUL-138300 This link opens in a new window
UDC:633
ISSN on article:2223-7747
DOI:10.3390/plants11131778 This link opens in a new window
COBISS.SI-ID:115302403 This link opens in a new window
Publication date in RUL:14.07.2022
Views:612
Downloads:82
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Record is a part of a journal

Title:Plants
Shortened title:Plants
Publisher:MDPI
ISSN:2223-7747
COBISS.SI-ID:523345433 This link opens in a new window

Licences

License:CC BY-NC 4.0, Creative Commons Attribution-NonCommercial 4.0 International
Link:http://creativecommons.org/licenses/by-nc/4.0/
Description:A creative commons license that bans commercial use, but the users don’t have to license their derivative works on the same terms.
Licensing start date:14.07.2022

Secondary language

Language:Slovenian
Keywords:dalmatinski bolhač, genetika, mikrosatelitski markerji, genetska raznolikost, SSR markerji

Projects

Funder:HRZZ - Croatian Science Foundation
Project number:IP-06-2016-9034
Name:Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium/Trevir./Sch. Bip.) insecticidal potential
Acronym:PyrDiv

Funder:ARRS - Slovenian Research Agency
Project number:P4-0077
Name:Kmetijske rastline - genetika in sodobne tehnologije

Funder:Other - Other funder or multiple funders
Funding programme:Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
Project number:KK.01.1.1.01.0005
Name:Biodiversity and Molecular Plant Breeding

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