The potential of HTS approaches for accurate genotyping in grapevine (Vitis vinifera L.)

Kunej, Urban (avtor), Dervishi, Aida (avtor), Laucou, Valérie (avtor), Jakše, Jernej (avtor), Štajner, Nataša (avtor)

The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.

• Jezik: Angleški jezik
• Ključne besede: Vitis vinifera L., microsatellites, high-throughput sequencing, SSR markers, genotyping
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: BF - Biotehniška fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2020
• Št. strani: 16 str.
• Številčenje: Vol. 11, iss. 8, art. 917
• PID: 20.500.12556/RUL-134355
• UDK: 577.2
• ISSN pri članku: 2073-4425
• DOI: 10.3390/genes11080917
• COBISS.SI-ID: 24967939
• Datum objave v RUL: 10.01.2022

Gradivo je del revije

• Naslov: Genes
• Skrajšan naslov: Genes
• Založnik: Multidisciplinary Digital Publishing Institute (MDPI)
• ISSN: 2073-4425
• COBISS.SI-ID: 523100185

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.
• Začetek licenciranja: 10.08.2020

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: Vitis vinifera, sorte, vinska trta, mikrosateliti, SSR markerji, genotipiziranje, sekvenciranje, molekularni markerji

Projekti

• Financer: ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
• Številka projekta: P4-0077
• Naslov: Kmetijske rastline - genetika in sodobne tehnologije