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The potential of HTS approaches for accurate genotyping in grapevine (Vitis vinifera L.)
ID
Kunej, Urban
(
Author
),
ID
Dervishi, Aida
(
Author
),
ID
Laucou, Valérie
(
Author
),
ID
Jakše, Jernej
(
Author
),
ID
Štajner, Nataša
(
Author
)
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https://www.mdpi.com/2073-4425/11/8/917
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Abstract
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.
Language:
English
Keywords:
Vitis vinifera L.
,
microsatellites
,
high-throughput sequencing
,
SSR markers
,
genotyping
Work type:
Article
Typology:
1.01 - Original Scientific Article
Organization:
BF - Biotechnical Faculty
Publication status:
Published
Publication version:
Version of Record
Year:
2020
Number of pages:
16 str.
Numbering:
Vol. 11, iss. 8, art. 917
PID:
20.500.12556/RUL-134355
UDC:
577.2
ISSN on article:
2073-4425
DOI:
10.3390/genes11080917
COBISS.SI-ID:
24967939
Publication date in RUL:
10.01.2022
Views:
736
Downloads:
147
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Record is a part of a journal
Title:
Genes
Shortened title:
Genes
Publisher:
Multidisciplinary Digital Publishing Institute (MDPI)
ISSN:
2073-4425
COBISS.SI-ID:
523100185
Licences
License:
CC BY 4.0, Creative Commons Attribution 4.0 International
Link:
http://creativecommons.org/licenses/by/4.0/
Description:
This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:
10.08.2020
Secondary language
Language:
Slovenian
Keywords:
Vitis vinifera
,
sorte
,
vinska trta
,
mikrosateliti
,
SSR markerji
,
genotipiziranje
,
sekvenciranje
,
molekularni markerji
Projects
Funder:
ARRS - Slovenian Research Agency
Project number:
P4-0077
Name:
Kmetijske rastline - genetika in sodobne tehnologije
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