Sterken Mark G, Bevers Roel P J, Volkers Rita J M, Riksen Joost A G, Kammenga Jan E, Snoek Basten L
Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands.
Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands.
Front Genet. 2020 Nov 3;11:501376. doi: 10.3389/fgene.2020.501376. eCollection 2020.
The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on and regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the - and 40% of the -eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60-93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for vs. eQTL and that the environment affects the eQTL micro-architecture.
利用近交群体中的自然变异对表达数量性状基因座（eQTL）进行研究，已获得了有关复杂性状转录调控的详细信息。使用重组自交系（RIL）对eQTL进行的研究，使人们对转录本丰度的调控位点有了深入了解。然而，确定潜在的因果多态基因或变异很困难，但对于理解复杂性状的调控网络来说最终又是必不可少的。这需要深入了解相关基因座是单个eQTL还是紧密连锁的eQTL组合，以及这种QTL微结构如何依赖于环境。我们通过使用渗入系（IL）的新数据，对先前在[具体内容缺失]中定位的eQTL进行独立复制测试，解决了这些问题。两个群体均表明，基因表达的总体遗传力、eQTL的数量和位置在不同环境中存在差异。在不同环境中，我们能够使用IL复制70%的[具体内容缺失] - eQTL和40%的[具体内容缺失] - eQTL。通过测试八种不同的模拟模型，我们发现加性效应在所有三种环境中对RIL/IL遗传力的解释高达60 - 93%。在对照环境中，紧密连锁的eQTL对RIL/IL遗传力的解释高达40%，而在热应激和恢复环境中仅为7%。总之，我们表明eQTL的可重复性在[具体内容缺失] - eQTL方面高于[具体内容缺失] - eQTL，并且环境会影响eQTL微结构。
