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Assessing myBaits Target Capture Sequencing Methodology Using Short-Read Sequencing for Variant Detection in Oat Genomics and Breeding

Mahmood, Khalid Mahmood; Sarup, Pernille; Oertelt, Lukas Oertelt; Jahoor, Ahmed and Orabi, Jihad (2024) Assessing myBaits Target Capture Sequencing Methodology Using Short-Read Sequencing for Variant Detection in Oat Genomics and Breeding. Genes 2024, 15, 700, 15 (700), pp. 1-18.

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Document available online at: https://www.mdpi.com/2806190


Summary in the original language of the document

The integration of target capture systems with next-generation sequencing has emerged as an efficient tool for exploring specific genetic regions with a high resolution and facilitating the rapid discovery of novel alleles. Despite these advancements, the application of targeted sequencing
methodologies, such as the myBaits technology, in polyploid oat species remains relatively unexplored. In this study, we utilized the myBaits target capture method offered by Daicel Arbor Biosciences to detect variants and assess their reliability for variant detection in oat genomics and
breeding. Ten oat genotypes were carefully chosen for targeted sequencing, focusing on specific regions on chromosome 2A to detect variants. The selected region harbors 98 genes. Precisely designed baits targeting the genes within these regions were employed for the target capture sequencing. We
employed various mappers and variant callers to identify variants. After the identification of variants, we focused on the variants identified via all variants callers to assess the applicability of the myBaits sequencing methodology in oat breeding. In our efforts to validate the identified variants, we focused on two SNPs, one deletion and one insertion identified via all variant callers in the genotypes KF-318 and NOS 819111-70 but absent in the remaining eight genotypes. The Sanger sequencing of targeted SNPs failed to reproduce target capture data obtained through the myBaits technology. Similarly, the validation of deletion and insertion variants via high-resolution melting (HRM) curve analysis also failed to reproduce target capture data, again suggesting limitations in the reliability of the myBaits target capture sequencing using short-read sequencing for variant detection in the oat genome. This study shed light on the importance of exercising caution when employing the myBaits target capture strategy for variant detection in oats. This study provides valuable insights for breeders seeking to advance oat breeding efforts and marker development using myBaits target capture sequencing, emphasizing the significance of methodological sequencing considerations in oat genomics research


EPrint Type:Journal paper
Keywords:oat genome; myBaits technology; targeted sequencing; variant calling; genetic variants; genomic regions
Agrovoc keywords:
Language
Value
URI
English
genomes
http://aims.fao.org/aos/agrovoc/c_3224
English
genetic variance
http://aims.fao.org/aos/agrovoc/c_71b35b92
Subjects: Crop husbandry > Breeding, genetics and propagation
Crop husbandry > Crop health, quality, protection
Research affiliation: Denmark > Organic RDD 7 > Oatganic
ISSN:15060700
DOI:https://doi.org/10.3390/ genes15060700
Deposited By: Haldrup, Mr. Hans
ID Code:53421
Deposited On:15 Jul 2024 13:50
Last Modified:15 Jul 2024 13:54
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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