Population genomics of honey bees reveals a selection signature indispensable for royal jelly production

Rizwan, Muhammad; Liang, Pingping; Ali, Habib; Li, Zhiguo; Nie, Hongyi; Saqib, Hafiz Sohaib Ahmed; Fiaz, Sajid; Raza, Muhammad Fahad; Hassanyar, Aqai Kalan; Niu, Qingsheng

doi:10.1016/j.mcp.2020.101542

Cited by 8 publications

(7 citation statements)

References 49 publications

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“…We further validated the successful SNPs in a large number of samples from various geographic locations to confirm their reliability. The use of these SNPs as valuable genetic markers in selective breeding programs for improving multiple honeybee traits, including SBV resistance, has been suggested in previous studies that found the same corresponding alleles related to SBV resistance, high royal jelly production, and chalk-brood resistance in A. melliferra [ 26 , 27 , 31 ].…”

Section: Discussionmentioning

confidence: 99%

“…Illumina sequencing is a precise platform that can generate millions of short-read sequences [ 30 ]. DNA resequencing using SNPs with F ST and population differentiation index (π) has been used to assess the high royal jelly production of the honeybee A. mellifera [ 31 ]. SNP molecular markers have also been used to examine genetic variations in honeybees that have undergone Africanization for ancestry assignments.…”

Section: Introductionmentioning

confidence: 99%

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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

Hassanyar

Nie

et al. 2023

IJMS

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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 (FST) 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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Hassanyar

Nie

et al. 2023

IJMS

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“…Population genomic analyses of the honey bee have already revealed strong signatures of positive selection on currently applied selection traits (e.g. royal jelly production; Rizwan et al ., 2020 ). In this study, we associated the Abscam gene with calmness.…”

Section: Discussionmentioning

confidence: 99%

Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole‐genome sequences

et al. 2021

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Summary The identification of quantitative trait loci (QTL) through genome‐wide association studies (GWAS) is a powerful method for unravelling the genetic background of selected traits and improving early‐stage predictions. In honey bees (Apis mellifera), past genetic analyses have particularly focused on individual queens and workers. In this study, we used pooled whole‐genome sequences to ascertain the genetic variation of the entire colony. In total, we sampled 216 Apis mellifera mellifera and 28 Apis mellifera carnica colonies. Different experts subjectively assessed the gentleness and calmness of the colonies using a standardised protocol. Conducting a GWAS for calmness on 211 purebred A. m. mellifera colonies, we identified three QTL, on chromosomes 8, 6, and 12. The two first QTL correspond to LOC409692 gene, coding for a disintegrin and metalloproteinase domain‐containing protein 10, and to Abscam gene, coding for a Dscam family member Abscam protein, respectively. The last gene has been reported to be involved in the domestication of A. mellifera. The third QTL is located 13 kb upstream of LOC102655631, coding for a trehalose transporter. For gentleness, two QTL were identified on chromosomes 4 and 3. They are located within gene LOC413669, coding for a lap4 protein, and gene LOC413416, coding for a bicaudal C homolog 1‐B protein, respectively. The identified positional candidate genes of both traits mainly affect the olfaction and nervous system of honey bees. Further research is needed to confirm the results and to better understand the genetic and phenotypic basis of calmness and gentleness.

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“…anatoliaca ( Koc et al, 2021 ). Unlike these bee races, RJBs have acquired adaptive properties over decades of selective breeding ( Altaye et al, 2019 ; Rizwan et al, 2020 ). Remarkably, RJB nurses have larger size of acini in hypopharyngeal glands ( Li et al, 2010 ) and have reshaped their proteomes of hypopharyngeal and mandibular glands, hemolymph, brain, and antennae to match the elevated RJ output ( Huo et al, 2016 ; Ararso et al, 2018 ; Hu et al, 2019b ; Wu et al, 2019 ; Zhang et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Effect of queen cell numbers on royal jelly production and quality

Ahmat

2022

Current Research in Food Science

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Population genomics of honey bees reveals a selection signature indispensable for royal jelly production

Cited by 8 publications

References 49 publications

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

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

Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole‐genome sequences

Effect of queen cell numbers on royal jelly production and quality

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