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Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Eklof, Helena and Bernhardsson, Carolina and Ingvarsson, Pär (2020). Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies. Forests. 11 , 1185
[Research article]

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Abstract

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

Authors/Creators:Eklof, Helena and Bernhardsson, Carolina and Ingvarsson, Pär
Title:Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies
Series Name/Journal:Forests
Year of publishing :2020
Volume:11
Article number:1185
Number of Pages:13
Publisher:MDPI
ISSN:1999-4907
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
Keywords:genetic diversity, genotyping, GBS, Norway spruce, Picea abies
URN:NBN:urn:nbn:se:slu:epsilon-p-109757
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-109757
Additional ID:
Type of IDID
DOI10.3390/f11111185
Web of Science (WoS)000594034500001
ID Code:21242
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:15 Jan 2021 10:23
Metadata Last Modified:15 Jan 2021 10:31

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