Data from: Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach
| Main Authors: | Li, Zitong, Guo, Baocheng, Yang, Jing, Herczeg, Gábor, Gonda, Abigél, Balázs, Gergely, Shikano, Takahito, Calboli, Federico C.F., Merilä, Juha, Calboli, Federico C. F. |
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| Format: | info dataset Journal |
| Terbitan: |
, 2016
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5011611 |
Daftar Isi:
- Quantitative 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.
- Data for QTL mapping on brain size in sticklebacksThe data set is used in a quantitative trait locus mapping study on six brain volume traits including bulbus olfactorious, telecephalon, optic tectum, hypothalamus, cerebellum and total brain size of a F2 nine stickleback population. The data consists of 239 individuals, and 15198 non-identical SNPs. A linkage map has been constructed, and divide the SNPs into 21 linkage groups. The data are distributed as following: File1: brain_phenotype.txt -The phenotype data of six brain traits, which have been corrected by the sex and bodysize effects. File2: genotype.txt -The SNP data, each row represents the individuals which is one-to-one match to the phenotype data file, and each column represents the SNPs which is one-to-one match to the linkage map file. The missing genotype data have been imputed, and coded as 1,0,-1 for the genotypes AA, AB and BB, respectively. File3: linkage_map.csv -The linkage map information, column1 is the marker ID, column2 is the linkage group info, and column3 is the linkage position of each SNPQTL_brain.zip