Department of Genetics.
Department of Computer Science.
G3 (Bethesda). 2019 May 7;9(5):1303-1311. doi: 10.1534/g3.119.400039.
Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts toward inbreeding undertaken by the UNC Systems Genetics Core. The timing reflects our competing mandates to release to the public as many CC strains as possible while achieving an acceptable level of inbreeding. The new six strains have a higher than average founder contribution from non- strains than the previously released CC strains. Five of the six strains also have high residual heterozygosity (>14%), which may be related to non- founder contributions. Finally, we report on updated estimates on residual heterozygosity across the entire CC population using a novel, simple and cost effective genotyping platform on three mice from each strain. We observe a reduction in residual heterozygosity across all previously released CC strains. We discuss the optimal use of different genetic resources available for the CC population.
重组近交系群体的两个关键特征是基因组特征明确和可重复性。在这里，我们报告了另外六个协作交叉（CC）品系的测序基因组和 72 个 CC 品系的近交进展。我们之前已经报告了 69 个 CC 品系的公开序列，使具有全基因组序列的 CC 品系总数达到 75 个。这六个 CC 品系的测序更新了 UNC 系统遗传学核心进行的近交工作。时间反映了我们的竞争任务，既要向公众发布尽可能多的 CC 品系，又要达到可接受的近交水平。新的六个品系比之前发布的 CC 品系具有更高的非品系创始人贡献。这六个品系中的五个也具有较高的残余杂合度（>14%），这可能与非创始人贡献有关。最后，我们使用每个品系的三只老鼠的新型简单且具有成本效益的基因分型平台，报告了整个 CC 群体中残余杂合度的最新估计值。我们观察到所有先前发布的 CC 品系的残余杂合度都有所降低。我们讨论了最佳利用 CC 群体中可用的不同遗传资源。
