A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)
Abstract With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are bec...
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Nature Portfolio
2021
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oai:doaj.org-article:3fb901d0402244f698dbe697b40e8c832021-12-02T18:46:59ZA SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)10.1038/s41598-021-94833-x2045-2322https://doaj.org/article/3fb901d0402244f698dbe697b40e8c832021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94833-xhttps://doaj.org/toc/2045-2322Abstract With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.Dora HenriquesAna R. LopesNor ChejanovskyAnne DalmonMariano HigesClara Jabal-UrielYves Le ConteMaritza Reyes-CarreñoVictoria SorokerRaquel Martín-HernándezM. Alice PintoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021) |
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Medicine R Science Q Dora Henriques Ana R. Lopes Nor Chejanovsky Anne Dalmon Mariano Higes Clara Jabal-Uriel Yves Le Conte Maritza Reyes-Carreño Victoria Soroker Raquel Martín-Hernández M. Alice Pinto A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.) |
| description |
Abstract With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee. |
| format |
article |
| author |
Dora Henriques Ana R. Lopes Nor Chejanovsky Anne Dalmon Mariano Higes Clara Jabal-Uriel Yves Le Conte Maritza Reyes-Carreño Victoria Soroker Raquel Martín-Hernández M. Alice Pinto |
| author_facet |
Dora Henriques Ana R. Lopes Nor Chejanovsky Anne Dalmon Mariano Higes Clara Jabal-Uriel Yves Le Conte Maritza Reyes-Carreño Victoria Soroker Raquel Martín-Hernández M. Alice Pinto |
| author_sort |
Dora Henriques |
| title |
A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.) |
| title_short |
A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.) |
| title_full |
A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.) |
| title_fullStr |
A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.) |
| title_full_unstemmed |
A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.) |
| title_sort |
snp assay for assessing diversity in immune genes in the honey bee (apis mellifera l.) |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/3fb901d0402244f698dbe697b40e8c83 |
| work_keys_str_mv |
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