mRNA-seq of individual genetically identical Caenorhabditis elegans adults

Individual phenotypic differences persist even in genetically identical individuals, although separating genetic and environmental causation is difficult or impossible in most organisms. To understand the basis of individual differences in the absence of genetic differences, we measured two quantitative reproductive traits in genetically identical young adult Caenorhabditis elegans roundworms in a shared environment and performed single-individual mRNA-seq on each worm. We identified hundreds of genes for which expression variation was strongly associated with reproductive traits, some of which depended on prior environmental experience and some of which was random. Multiple small sets of genes together were highly predictive of reproductive traits across individuals. In the P0 generation, adult C. elegans hermaphrodites were allowed to lay progeny at day 1 or day 3 of adulthood. F1 progeny were then left at 20C throughout their life or shifted to 25C for 8 hours early in life. It was documented when each F1 worm reached egg-laying onset, and 24 hours after egg-laying onset, each F1 young adult worm was collected for individual worm mRNA-seq. The number of progeny laid in the first 24 hours was also measured for each worm.

即使遗传背景完全一致的个体间仍存在个体表型差异，但在多数生物体中，区分遗传与环境的因果成因往往困难乃至无法实现。为探究无遗传差异时个体差异的形成基础，我们在共享培养环境中，对遗传背景一致的年轻成年秀丽隐杆线虫（Caenorhabditis elegans）开展了两项定量生殖性状测量，并对每一条线虫进行单个体mRNA测序（mRNA-seq）。我们鉴定出数百个基因，其表达变异与生殖性状显著相关，其中部分变异依赖于既往环境经历，另有部分属于随机变异。多个小型基因集合联合即可高度预测个体间的生殖性状差异。在亲本代（P0）中，我们让成年雌雄同体秀丽隐杆线虫在成虫第1天或第3天产卵。随后将F1子代全程置于20℃环境中培养，或在其生命早期转移至25℃环境处理8小时。我们记录了每只F1线虫的产卵起始时间，并在产卵开始后24小时，收集每只F1年轻成虫以开展单个体mRNA测序。同时还测量了每只线虫最初24小时内的产卵数量。