Data from: Association between nucleotide variation in Efgr and wing shape in Drosophila melanogaster

As part of an effort to dissect quantitative trait locus effects to the nucleotide level, association was assessed between 238 single-nucleotide and 20 indel polymorphisms spread over 11 kb of the Drosophila melanogaster Egfr locus and nine relative warp measures of wing shape. One SNP in a conserved potential regulatory site for a GAGA factor in the promoter of alternate first exon 2 approaches conservative experimentwise significance (P < 0.00003) in the sample of 207 lines for association with the location of the crossveins in the central region of the wing. Several other sites indicate marginal association with one or more other aspects of shape. No strong effects of sex or population of origin were detected with measures of shape, but two different sites were strongly associated with overall wing size in interaction with these fixed factors. Whole-gene sequencing in very large samples, rather than selective genotyping, would appear to be the only strategy likely to be successful for detecting subtle associations in species with high polymorphism and little haplotype structure. However, these features severely limit the ability of linkage disequilibrium mapping in Drosophila to resolve quantitative effects to single nucleotides.

本研究为将数量性状位点（quantitative trait locus, QTL）的效应拆解至核苷酸分辨率水平，针对分布于黑腹果蝇（Drosophila melanogaster）Egfr基因座11 kb基因组区域内的238个单核苷酸多态性（single-nucleotide polymorphism, SNP）与20个插入缺失多态性（insertion-deletion polymorphism, indel），结合9项翅膀形态相对扭曲度量指标开展关联分析。在针对207个果蝇品系的检测中，位于可变第一外显子2启动子内、保守的GAGA因子潜在调控位点中的1个SNP，在与翅膀中央区域翅横脉位置的关联分析中接近保守型实验整体显著性阈值（P < 0.00003）。其余多个位点与一项或多项其他翅膀形态特征存在边际关联。未检测到性别或起源群体对翅膀形态度量存在显著效应，但存在两个不同位点与整体翅膀大小存在显著关联，且该关联受上述固定效应因素的交互调控。相较于选择性基因分型，大样本全基因测序策略似乎是在多态性水平较高且单倍型结构较弱的物种中检测细微关联的唯一可行方案。然而，这些特征极大限制了果蝇中连锁不平衡（linkage disequilibrium, LD）定位将数量效应拆解至单个核苷酸分辨率的能力。