RIL genotype probability table.

The genes for ribosomal RNA (rRNA) are encoded by ribosomal DNA (rDNA), whose structure is notable for being present in arrays of tens to thousands of tandemly repeated copies in eukaryotic genomes. The exact number of rDNA copies per genome is highly variable within a species, with differences between individuals measuring in potentially hundreds of copies and megabases of DNA. The extent to which natural variation in rDNA copy number impacts whole-organism phenotypes such as fitness and lifespan is poorly understood, in part due to difficulties in manipulating such large and repetitive tracts of DNA even in model organisms. Here, we used the natural resource of copy number variation in C. elegans wild isolates to generate new tools and investigated the phenotypic consequences of this variation. Specifically, we generated a panel of recombinant inbred lines (RILs) using a laboratory strain derivative with ~130 haploid rDNA copies and a wild isolate with ~417 haploid rDNA copies, one of the highest validated C. elegans rDNA copy number arrays. We find that rDNA copy number is stable in the RILs, rejecting prior hypotheses that predicted copy number instability and copy number reversion. To isolate effects of rDNA copy number on phenotype, we produced a series of near isogenic lines (NILs) with rDNA copy numbers representing the high and low end of the rDNA copy number spectrum in C. elegans wild isolates. We find no correlation between rDNA copy number and phenotypes of rRNA abundance, competitive fitness, early life fertility, lifespan, or global transcriptome under standard laboratory conditions. These findings demonstrate a remarkable ability of C. elegans to tolerate substantial variation in a locus critical to fundamental cell function. Our study provides strain resources for future investigations into the boundaries of this tolerance.

核糖体RNA（ribosomal RNA, rRNA）的基因由核糖体DNA（ribosomal DNA, rDNA）编码，其结构的显著特征为在真核生物基因组中以数十至数千个串联重复拷贝的阵列形式存在。每个基因组中rDNA拷贝的精确数量在同一物种内存在高度变异，不同个体间的差异可高达数百个拷贝，对应的DNA片段长度可达数兆碱基。目前，rDNA拷贝数的自然变异对适合度、寿命等生物体整体表型的影响程度仍不甚明晰，部分原因在于即便在模式生物中，操纵这类庞大且重复的DNA区域也存在诸多困难。本研究利用秀丽隐杆线虫（Caenorhabditis elegans, C. elegans）野生分离株的拷贝数变异这一天然资源，开发了全新研究工具，并探究了该拷贝数变异的表型效应。具体而言，我们利用一株携带约130个单倍体rDNA拷贝的实验室菌株衍生株，与一株携带约417个单倍体rDNA拷贝的野生分离株——后者是已验证的rDNA拷贝数阵列最高的秀丽隐杆线虫菌株之一——构建了重组近交系（recombinant inbred lines, RILs）群体。研究发现，RILs中的rDNA拷贝数保持稳定，推翻了此前预测拷贝数不稳定及会发生拷贝数回复的假说。为了分离rDNA拷贝数对表型的影响，我们构建了一系列近等基因系（near isogenic lines, NILs），其rDNA拷贝数覆盖了秀丽隐杆线虫野生分离株中rDNA拷贝数谱的高低两端。在标准实验室条件下，我们未发现rDNA拷贝数与rRNA丰度、竞争适合度、早期生育力、寿命或全局转录组等表型存在相关性。上述发现表明，秀丽隐杆线虫具备显著的耐受能力，可在对细胞基本功能至关重要的位点上容忍大幅的拷贝数变异。本研究为后续探究这类耐受能力的边界提供了菌株资源。