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Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing

Sacbrood virus (SBV) is a significant problem that impedes brood development in both eastern and western honeybees. Whole-genome sequencing has become an important tool in researching population genetic variations. Numerous studies have been conducted using multiple techniques to suppress SBV infect...

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Autores principales: Hassanyar, Aqai Kalan, Nie, Hongyi, Li, Zhiguo, Lin, Yan, Huang, Jingnan, Woldegiorgis, Samuel Tareke, Hussain, Mubasher, Feng, Wangjiang, Zhang, Zhaonan, Yu, Kejun, Su, Songkun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10094193/
https://www.ncbi.nlm.nih.gov/pubmed/37047210
http://dx.doi.org/10.3390/ijms24076238
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author Hassanyar, Aqai Kalan
Nie, Hongyi
Li, Zhiguo
Lin, Yan
Huang, Jingnan
Woldegiorgis, Samuel Tareke
Hussain, Mubasher
Feng, Wangjiang
Zhang, Zhaonan
Yu, Kejun
Su, Songkun
author_facet Hassanyar, Aqai Kalan
Nie, Hongyi
Li, Zhiguo
Lin, Yan
Huang, Jingnan
Woldegiorgis, Samuel Tareke
Hussain, Mubasher
Feng, Wangjiang
Zhang, Zhaonan
Yu, Kejun
Su, Songkun
author_sort Hassanyar, Aqai Kalan
collection PubMed
description Sacbrood virus (SBV) is a significant problem that impedes brood development in both eastern and western honeybees. Whole-genome sequencing has become an important tool in researching population genetic variations. Numerous studies have been conducted using multiple techniques to suppress SBV infection in honeybees, but the genetic markers and molecular mechanisms underlying SBV resistance have not been identified. To explore single nucleotide polymorphisms (SNPs), insertions, deletions (Indels), and genes at the DNA level related to SBV resistance, we conducted whole-genome resequencing on 90 Apis cerana cerana larvae raised in vitro and challenged with SBV. After filtering, a total of 337.47 gigabytes of clean data and 31,000,613 high-quality SNP loci were detected in three populations. We used ten databases to annotate 9359 predicted genes. By combining population differentiation index (F(ST)) and nucleotide polymorphisms (π), we examined genome variants between resistant (R) and susceptible (S) larvae, focusing on site integrity (INT < 0.5) and minor allele frequency (MAF < 0.05). A selective sweep analysis with the top 1% and top 5% was used to identify significant regions. Two SNPs on the 15th chromosome with GenBank KZ288474.1_322717 (Guanine > Cytosine) and KZ288479.1_95621 (Cytosine > Thiamine) were found to be significantly associated with SBV resistance based on their associated allele frequencies after SNP validation. Each SNP was authenticated in 926 and 1022 samples, respectively. The enrichment and functional annotation pathways from significantly predicted genes to SBV resistance revealed immune response processes, signal transduction mechanisms, endocytosis, peroxisomes, phagosomes, and regulation of autophagy, which may be significant in SBV resistance. This study presents novel and useful SNP molecular markers that can be utilized as assisted molecular markers to select honeybees resistant to SBV for breeding and that can be used as a biocontrol technique to protect honeybees from SBV.
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spelling pubmed-100941932023-04-13 Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing Hassanyar, Aqai Kalan Nie, Hongyi Li, Zhiguo Lin, Yan Huang, Jingnan Woldegiorgis, Samuel Tareke Hussain, Mubasher Feng, Wangjiang Zhang, Zhaonan Yu, Kejun Su, Songkun Int J Mol Sci Article Sacbrood virus (SBV) is a significant problem that impedes brood development in both eastern and western honeybees. Whole-genome sequencing has become an important tool in researching population genetic variations. Numerous studies have been conducted using multiple techniques to suppress SBV infection in honeybees, but the genetic markers and molecular mechanisms underlying SBV resistance have not been identified. To explore single nucleotide polymorphisms (SNPs), insertions, deletions (Indels), and genes at the DNA level related to SBV resistance, we conducted whole-genome resequencing on 90 Apis cerana cerana larvae raised in vitro and challenged with SBV. After filtering, a total of 337.47 gigabytes of clean data and 31,000,613 high-quality SNP loci were detected in three populations. We used ten databases to annotate 9359 predicted genes. By combining population differentiation index (F(ST)) and nucleotide polymorphisms (π), we examined genome variants between resistant (R) and susceptible (S) larvae, focusing on site integrity (INT < 0.5) and minor allele frequency (MAF < 0.05). A selective sweep analysis with the top 1% and top 5% was used to identify significant regions. Two SNPs on the 15th chromosome with GenBank KZ288474.1_322717 (Guanine > Cytosine) and KZ288479.1_95621 (Cytosine > Thiamine) were found to be significantly associated with SBV resistance based on their associated allele frequencies after SNP validation. Each SNP was authenticated in 926 and 1022 samples, respectively. The enrichment and functional annotation pathways from significantly predicted genes to SBV resistance revealed immune response processes, signal transduction mechanisms, endocytosis, peroxisomes, phagosomes, and regulation of autophagy, which may be significant in SBV resistance. This study presents novel and useful SNP molecular markers that can be utilized as assisted molecular markers to select honeybees resistant to SBV for breeding and that can be used as a biocontrol technique to protect honeybees from SBV. MDPI 2023-03-25 /pmc/articles/PMC10094193/ /pubmed/37047210 http://dx.doi.org/10.3390/ijms24076238 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hassanyar, Aqai Kalan
Nie, Hongyi
Li, Zhiguo
Lin, Yan
Huang, Jingnan
Woldegiorgis, Samuel Tareke
Hussain, Mubasher
Feng, Wangjiang
Zhang, Zhaonan
Yu, Kejun
Su, Songkun
Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing
title Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing
title_full Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing
title_fullStr Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing
title_full_unstemmed Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing
title_short Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing
title_sort discovery of snp molecular markers and candidate genes associated with sacbrood virus resistance in apis cerana cerana larvae by whole-genome resequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10094193/
https://www.ncbi.nlm.nih.gov/pubmed/37047210
http://dx.doi.org/10.3390/ijms24076238
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