QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline

Transposable elements (TEs) are obligate genetic parasites that propagate in host genomes by replicating in germline nuclei, thereby ensuring transmission to offspring. This selfish replication not only produces deleterious mutations—in extreme cases, TE mobilization induces genotoxic stress that prohibits the production of viable gametes. Host genomes could reduce these fitness effects in two ways: resistance and tolerance. Resistance to TE propagation is enacted by germline-specific small-RNA-mediated silencing pathways, such as the Piwi-interacting RNA (piRNA) pathway, and is studied extensively. However, it remains entirely unknown whether host genomes may also evolve tolerance by desensitizing gametogenesis to the harmful effects of TEs. In part, the absence of research on tolerance reflects a lack of opportunity, as small-RNA-mediated silencing evolves rapidly after a new TE invades, thereby masking existing variation in tolerance. We have exploited the recent historical invasion of the Drosophila melanogaster genome by P-element DNA transposons in order to study tolerance of TE activity. In the absence of piRNA-mediated silencing, the genotoxic stress imposed by P-elements disrupts oogenesis and, in extreme cases, leads to atrophied ovaries that completely lack germline cells. By performing quantitative trait locus (QTL) mapping on a panel of recombinant inbred lines (RILs) that lack piRNA-mediated silencing of P-elements, we uncovered multiple QTL that are associated with differences in tolerance of oogenesis to P-element transposition. We localized the most significant QTL to a small 230-kb euchromatic region, with the logarithm of the odds (LOD) peak occurring in the bruno locus, which codes for a critical and well-studied developmental regulator of oogenesis. Genetic, cytological, and expression analyses suggest that bruno dosage modulates germline stem cell (GSC) loss in the presence of P-element activity. Our observations reveal segregating variation in TE tolerance for the first time, and implicate gametogenic regulators as a source of tolerant variants in natural populations.

转座因子（Transposable Elements, TEs）是专性遗传寄生物，通过在宿主生殖系细胞核内复制实现基因组内增殖，从而确保其传递给子代。这种自私性复制不仅会产生有害突变，极端情况下，转座因子的转座还会引发遗传毒性应激，阻碍可育配子的生成。宿主基因组可通过两种途径降低这些适合度成本：抗性与耐受。对转座因子转座的抗性由生殖系特异性小RNA介导的沉默通路介导，例如Piwi互作RNA（Piwi-interacting RNA, piRNA）通路，该机制已被广泛研究。然而，宿主基因组是否可通过使配子发生对转座因子的有害效应脱敏，从而演化出耐受策略，目前仍完全未知。目前对耐受机制研究的缺失，一定程度上源于研究契机不足：新转座因子入侵后，小RNA介导的沉默会快速演化，从而掩盖了已存在的耐受变异。本研究借助黑腹果蝇（Drosophila melanogaster）基因组近期被P因子DNA转座子入侵的历史模型，开展转座因子活性耐受的相关研究。当缺乏piRNA介导的沉默时，P因子引发的遗传毒性应激会破坏卵子发生，极端情况下会导致卵巢萎缩且完全缺失生殖系细胞。本研究对一组缺失P因子piRNA介导沉默的重组自交系（Recombinant Inbred Lines, RILs）开展数量性状基因座（Quantitative Trait Locus, QTL）定位，发现多个与卵子发生对P因子转座的耐受差异相关的QTL。我们将最显著的QTL定位至一个230kb的小型常染色质区域，其对数似然比（Logarithm of the Odds, LOD）峰值位于bruno基因座，该基因编码一个关键且被广泛研究的卵子发生发育调控因子。遗传学、细胞学与表达分析结果显示，bruno的基因剂量可调控P因子活性存在时生殖系干细胞（Germline Stem Cell, GSC）的丢失情况。本研究首次揭示了转座因子耐受的分离变异，并证实配子发生调控因子是自然种群中耐受变异的来源之一。