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

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

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.

• Jezik: Angleški jezik
• Ključne besede: Tanacetum cinerariifolium, Dalmatian pyrethrum, Asteraceae, genomic SSRs, microsatellite markers, SSR markers
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: BF - Biotehniška fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2022
• Št. strani: 11 str.
• Številčenje: Vol. 11, iss. 13, art. 1778
• PID: 20.500.12556/RUL-138300
• UDK: 633
• ISSN pri članku: 2223-7747
• DOI: 10.3390/plants11131778
• COBISS.SI-ID: 115302403
• Datum objave v RUL: 14.07.2022

Gradivo je del revije

• Naslov: Plants
• Skrajšan naslov: Plants
• Založnik: MDPI
• ISSN: 2223-7747
• COBISS.SI-ID: 523345433

Licence

• Licenca: CC BY-NC 4.0, Creative Commons Priznanje avtorstva-Nekomercialno 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by-nc/4.0/deed.sl
• Opis: Licenca Creative Commons, ki prepoveduje komercialno uporabo, vendar uporabniki ne rabijo upravljati materialnih avtorskih pravic na izpeljanih delih z enako licenco.
• Začetek licenciranja: 14.07.2022

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: dalmatinski bolhač, genetika, mikrosatelitski markerji, genetska raznolikost, SSR markerji