Data from: Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach

dc.contributor.affiliationUniversity of Helsinki - Li, Zitong
dc.contributor.affiliationUniversity of Helsinki - Guo, Baocheng
dc.contributor.affiliationUniversity of Helsinki - Yang, Jing
dc.contributor.affiliationUniversity of Helsinki - Herczeg, Gábor
dc.contributor.affiliationUniversity of Helsinki - Gonda, Abigél
dc.contributor.affiliationEötvös Loránd University - Balázs, Gergely
dc.contributor.affiliationUniversity of Helsinki - Shikano, Takahito
dc.contributor.affiliationUniversity of Helsinki - Calboli, Federico C.F.
dc.contributor.affiliationUniversity of Helsinki - Merilä, Juha
dc.contributor.affiliationUniversity of Helsinki - Calboli, Federico C. F.
dc.contributor.authorLi, Zitong
dc.contributor.authorGuo, Baocheng
dc.contributor.authorYang, Jing
dc.contributor.authorHerczeg, Gábor
dc.contributor.authorGonda, Abigél
dc.contributor.authorBalázs, Gergely
dc.contributor.authorShikano, Takahito
dc.contributor.authorCalboli, Federico C.F.
dc.contributor.authorMerilä, Juha
dc.contributor.authorCalboli, Federico C. F.
dc.coverage.spatialFinland
dc.coverage.spatialNordic Europe
dc.date.accessioned2025-03-24T15:11:42Z
dc.date.issued2016-12-19
dc.date.issued2016-12-19
dc.descriptionQuantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multi-locus QTL mapping approaches based on a de-biased LASSO method. Apart from having more statistical power to detect QTL and reduced rate of false positives than conventional QTL mapping approaches, the developed methods can handle large marker panels and provide estimates of genomic heritability. Single-locus analyses of an F2-interpopulation cross with 239 individuals and 15 198 fully informative single nucleotide polymorphisms (SNPs) uncovered 79 QTL associated with variation in stickleback brain size traits. Many of these loci were in strong linkage disequilibrium (LD) with each other, and consequently, a multi-locus mapping of individual SNPs, accounting for LD structure in the data, recovered only four significant QTL. However, a multi-locus mapping of SNPs grouped by linkage group (LG) identified 14 LGs (1-6 depending on the trait) that influence variation in brain traits. For instance, 17.6% of the variation in relative brain size was explainable by cumulative effects of SNPs distributed over six LGs, whereas 42% of the variation was accounted for by all 21 LGs. Hence, the results suggest that variation in stickleback brain traits is influenced by many small-effect loci. Apart from suggesting moderately heritable (h2 ≈ 0.15-0.42) multifactorial genetic architecture of brain traits, the results highlight the challenges in identifying the loci contributing to variation in quantitative traits. Nevertheless, the results demonstrate that the novel QTL mapping approach developed here has distinctive advantages over the traditional QTL mapping methods in analyses of dense marker panels.
dc.identifierhttps://doi.org/10.5061/dryad.gn44q
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/9327
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectquantitative trait loci
dc.subjectDe-biased LASSO
dc.subjectMultiple-locus mapping
dc.subjectPungitius pungitius
dc.subjectBrain size
dc.titleData from: Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach
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