Development of microsatellite markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a plant with a large and highly repetitive genome

Varga, Filip (author), Liber, Zlatko (author), Jakše, Jernej (author), Turudić, Ante (author), Šatović, Zlatko (author), Radosavljević, Ivan (author), Jeran, Nina (author), Grdiša, Martina (author)

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
• UDC: 633
• ISSN on article: 2223-7747
• DOI: 10.3390/plants11131778
• COBISS.SI-ID: 115302403
• Publication date in RUL: 14.07.2022

Record is a part of a journal

• Title: Plants
• Shortened title: Plants
• Publisher: MDPI
• ISSN: 2223-7747
• COBISS.SI-ID: 523345433

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